The cytoscape-clj Reference Manual

This is the cytoscape-clj Reference Manual, version 0.2.18, generated automatically by Declt version 4.0 beta 2 "William Riker" on Mon Feb 26 16:11:38 2024 GMT+0.

Table of Contents


1 Introduction


2 Systems

The main system appears first, followed by any subsystem dependency.


2.1 cytoscape-clj

A cytoscape widget for Common Lisp Jupyter.

Author

Tarn W. Burton

License

MIT

Version

0.2.18

Defsystem Dependency

jupyter-lab-extension (system).

Dependency

common-lisp-jupyter (system).

Source

cytoscape-clj.asd.

Child Components

3 Modules

Modules are listed depth-first from the system components tree.


3.1 cytoscape-clj/src

Source

cytoscape-clj.asd.

Parent Component

cytoscape-clj (system).

Child Components

4 Files

Files are sorted by type and then listed depth-first from the systems components trees.


4.1 Lisp


4.1.1 cytoscape-clj/cytoscape-clj.asd

Source

cytoscape-clj.asd.

Parent Component

cytoscape-clj (system).

ASDF Systems

cytoscape-clj.


4.1.2 cytoscape-clj/src/packages.lisp

Source

cytoscape-clj.asd.

Parent Component

src (module).

Packages

cytoscape.


4.1.3 cytoscape-clj/src/version.lisp

Dependency

packages.lisp (file).

Source

cytoscape-clj.asd.

Parent Component

src (module).

Internals

4.1.4 cytoscape-clj/src/common-slots.lisp

Dependency

version.lisp (file).

Source

cytoscape-clj.asd.

Parent Component

src (module).

Public Interface
Internals

4.1.5 cytoscape-clj/src/context-menu.lisp

Dependency

common-slots.lisp (file).

Source

cytoscape-clj.asd.

Parent Component

src (module).

Public Interface
Internals

4.1.6 cytoscape-clj/src/graph-layout.lisp

Dependency

context-menu.lisp (file).

Source

cytoscape-clj.asd.

Parent Component

src (module).

Public Interface
Internals

4.1.7 cytoscape-clj/src/cytoscape.lisp

Dependency

graph-layout.lisp (file).

Source

cytoscape-clj.asd.

Parent Component

src (module).

Public Interface
Internals

4.2 Other


4.2.1 cytoscape-clj/cytoscape-clj.lab-extension

Source

cytoscape-clj.asd.

Parent Component

cytoscape-clj (system).


5 Packages

Packages are listed by definition order.


5.1 cytoscape

Source

packages.lisp.

Use List

common-lisp.

Public Interface
Internals

6 Definitions

Definitions are sorted by export status, category, package, and then by lexicographic order.


6.1 Public Interface


6.1.1 Ordinary functions

Function: center (instance)
Package

cytoscape.

Source

cytoscape.lisp.

Function: fit-elements (instance &key elements padding)
Package

cytoscape.

Source

cytoscape.lisp.

Function: layout (instance)
Package

cytoscape.

Source

cytoscape.lisp.

Function: make-breadth-first-layout (&rest initargs &key spacing-factor node-dimensions-include-labels avoid-overlap animation-duration animation-easing animate fit padding bounding-box comm-id on-close selector on-layout-stop circle directed grid maximal roots &allow-other-keys)
Package

cytoscape.

Source

graph-layout.lisp.

Function: make-circle-layout (&rest initargs &key clockwise start-angle sweep spacing-factor node-dimensions-include-labels avoid-overlap animation-duration animation-easing animate fit padding bounding-box comm-id on-close selector on-layout-stop radius &allow-other-keys)
Package

cytoscape.

Source

graph-layout.lisp.

Function: make-cola-layout (&rest initargs &key randomize refresh node-dimensions-include-labels avoid-overlap animate fit padding bounding-box comm-id on-close selector on-layout-stop alignment all-const-iter convergence-threshold edge-jaccard-length edge-length edge-sym-diff-length flow gap-inequalities handle-disconnected max-simulation-time unconst-iter ungrabify-while-simulating user-const-iter &allow-other-keys)
Package

cytoscape.

Source

graph-layout.lisp.

Function: make-concentric-layout (&rest initargs &key clockwise start-angle sweep spacing-factor node-dimensions-include-labels avoid-overlap animation-duration animation-easing animate fit padding bounding-box comm-id on-close selector on-layout-stop equidistant min-node-spacing &allow-other-keys)
Package

cytoscape.

Source

graph-layout.lisp.

Function: make-context-menu (&rest initargs &key comm-id on-close menu-radius selector commands fill-color active-fill-color active-padding indicator-size separator-width spotlight-padding min-spotlight-radius max-spotlight-radius open-menu-events item-color item-text-shadow-color z-index at-mouse &allow-other-keys)
Package

cytoscape.

Source

context-menu.lisp.

Function: make-cose-layout (&rest initargs &key gravity num-iter nesting-factor randomize refresh node-dimensions-include-labels animation-duration animation-easing animate fit padding bounding-box comm-id on-close selector on-layout-stop component-spacing cooling-factor edge-elasticity ideal-edge-length initial-temp min-temp node-overlap node-repulsion &allow-other-keys)
Package

cytoscape.

Source

graph-layout.lisp.

Function: make-cytoscape-widget (&rest initargs &key comm-id on-close layout tabbable tooltip min-zoom max-zoom zooming-enabled user-zooming-enabled panning-enabled user-panning-enabled box-selection-enabled selection-type touch-tap-threshold desktop-tap-threshold autolock auto-ungrabify auto-unselectify headless style-enabled hide-edges-on-viewport texture-on-viewport motion-blur motion-blur-opacity wheel-sensitivity graph-layouts graph-style pan zoom elements context-menus &allow-other-keys)
Package

cytoscape.

Source

cytoscape.lisp.

Function: make-dagre-layout (&rest initargs &key spacing-factor node-dimensions-include-labels animation-duration animation-easing animate fit padding bounding-box comm-id on-close selector on-layout-stop edge-sep edge-weight min-length node-sep rank-dir ranker rank-sep &allow-other-keys)
Package

cytoscape.

Source

graph-layout.lisp.

Function: make-element (&rest initargs &key comm-id on-close group removed selected selectable locked grabbed grabbable classes data position &allow-other-keys)
Package

cytoscape.

Source

cytoscape.lisp.

Function: make-fcose-layout (&rest initargs &key randomize num-iter node-dimensions-include-labels nesting-factor gravity animate fit padding animation-duration animation-easing comm-id on-close selector on-layout-stop quality uniform-node-dimensions pack-components sampling-type sample-size node-separation pi-tol node-repulsion ideal-edge-length edge-elasticity tile tile-padding-vertical tile-padding-horizontal gravity-range-compound gravity-range gravity-compound initial-energy-on-incremental &allow-other-keys)
Package

cytoscape.

Source

graph-layout.lisp.

Function: make-graph-layout (&rest initargs &key comm-id on-close selector on-layout-stop &allow-other-keys)
Package

cytoscape.

Source

graph-layout.lisp.

Function: make-grid-layout (&rest initargs &key spacing-factor node-dimensions-include-labels avoid-overlap animation-duration animation-easing animate fit padding bounding-box comm-id on-close selector on-layout-stop avoid-overlap-padding cols condense rows &allow-other-keys)
Package

cytoscape.

Source

graph-layout.lisp.

Function: make-klay-layout (&rest initargs &key node-dimensions-include-labels animation-duration animation-easing animate fit padding comm-id on-close selector on-layout-stop add-unnecessary-bendpoints aspect-ratio border-spacing compact-components crossing-minimization cycle-breaking direction edge-routing edge-spacing-factor feedback-edges fixed-alignment in-layer-spacing-factor layout-hierarchy linear-segments-deflection-dampening merge-edges merge-hierarchy-crossing-edges node-layering node-placement randomization-seed route-self-loop-inside separate-connected-components spacing thoroughness &allow-other-keys)
Package

cytoscape.

Source

graph-layout.lisp.

Function: make-menu-command (&rest initargs &key comm-id on-close fill-color content content-style enabled on-select &allow-other-keys)
Package

cytoscape.

Source

context-menu.lisp.

Function: make-null-layout (&rest initargs &key comm-id on-close selector on-layout-stop &allow-other-keys)
Package

cytoscape.

Source

graph-layout.lisp.

Function: make-preset-layout (&rest initargs &key animation-duration animation-easing animate fit padding comm-id on-close selector on-layout-stop pan zoom &allow-other-keys)
Package

cytoscape.

Source

graph-layout.lisp.

Function: make-random-layout (&rest initargs &key animation-duration animation-easing animate fit padding bounding-box comm-id on-close selector on-layout-stop &allow-other-keys)
Package

cytoscape.

Source

graph-layout.lisp.

Function: on-layout-stop (widget handler)
Package

cytoscape.

Source

graph-layout.lisp.

Function: on-menu-command-select (widget handler)

Add a new selection handler for a menu command.

Package

cytoscape.

Source

context-menu.lisp.

Function: reset (instance)
Package

cytoscape.

Source

cytoscape.lisp.

Function: toggle-fullscreen (instance)
Package

cytoscape.

Source

cytoscape.lisp.


6.1.2 Generic functions

Generic Reader: %on-layout-stop (object)
Package

cytoscape.

Methods
Reader Method: %on-layout-stop ((graph-layout graph-layout))

automatically generated reader method

Source

graph-layout.lisp.

Target Slot

on-layout-stop.

Generic Writer: (setf %on-layout-stop) (object)
Package

cytoscape.

Methods
Writer Method: (setf %on-layout-stop) ((graph-layout graph-layout))

automatically generated writer method

Source

graph-layout.lisp.

Target Slot

on-layout-stop.

Generic Reader: active-fill-color (object)
Generic Writer: (setf active-fill-color) (object)
Package

cytoscape.

Methods
Reader Method: active-fill-color ((context-menu context-menu))
Writer Method: (setf active-fill-color) ((context-menu context-menu))

the colour used to indicate the selected command

Source

context-menu.lisp.

Target Slot

active-fill-color.

Generic Reader: active-padding (object)
Generic Writer: (setf active-padding) (object)
Package

cytoscape.

Methods
Reader Method: active-padding ((context-menu context-menu))
Writer Method: (setf active-padding) ((context-menu context-menu))

additional size in pixels for the active command

Source

context-menu.lisp.

Target Slot

active-padding.

Generic Function: add-graph (instance value &rest args)

Add a graph to a cytoscape widget based on value type.

Package

cytoscape.

Source

cytoscape.lisp.

Methods
Method: add-graph (instance (value hash-table) &rest args)
Method: add-graph (instance (value list) &rest args)
Generic Reader: add-unnecessary-bendpoints (object)
Generic Writer: (setf add-unnecessary-bendpoints) (object)
Package

cytoscape.

Methods
Reader Method: add-unnecessary-bendpoints ((klay-layout klay-layout))
Writer Method: (setf add-unnecessary-bendpoints) ((klay-layout klay-layout))
Source

graph-layout.lisp.

Target Slot

add-unnecessary-bendpoints.

Generic Reader: alignment (object)
Generic Writer: (setf alignment) (object)
Package

cytoscape.

Methods
Reader Method: alignment ((cola-layout cola-layout))
Writer Method: (setf alignment) ((cola-layout cola-layout))

Relative alignment constraints on nodes. Can also be set per node via data.

Source

graph-layout.lisp.

Target Slot

alignment.

Generic Reader: all-const-iter (object)
Generic Writer: (setf all-const-iter) (object)
Package

cytoscape.

Methods
Reader Method: all-const-iter ((cola-layout cola-layout))
Writer Method: (setf all-const-iter) ((cola-layout cola-layout))

Initial layout iterations with all constraints including non-overlap

Source

graph-layout.lisp.

Target Slot

all-const-iter.

Generic Reader: animate (object)
Generic Writer: (setf animate) (object)
Package

cytoscape.

Methods
Reader Method: animate ((common-slots common-slots))
Writer Method: (setf animate) ((common-slots common-slots))

Whether to animate changes to the layout

Source

common-slots.lisp.

Target Slot

animate.

Generic Reader: animation-duration (object)
Generic Writer: (setf animation-duration) (object)
Package

cytoscape.

Methods
Reader Method: animation-duration ((animation-slots animation-slots))
Writer Method: (setf animation-duration) ((animation-slots animation-slots))

Duration of animation in ms, if enabled

Source

common-slots.lisp.

Target Slot

animation-duration.

Generic Reader: animation-easing (object)
Generic Writer: (setf animation-easing) (object)
Package

cytoscape.

Methods
Reader Method: animation-easing ((animation-slots animation-slots))
Writer Method: (setf animation-easing) ((animation-slots animation-slots))

Easing of animation, if enabled

Source

common-slots.lisp.

Target Slot

animation-easing.

Generic Reader: aspect-ratio (object)
Generic Writer: (setf aspect-ratio) (object)
Package

cytoscape.

Methods
Reader Method: aspect-ratio ((klay-layout klay-layout))
Writer Method: (setf aspect-ratio) ((klay-layout klay-layout))
Source

graph-layout.lisp.

Target Slot

aspect-ratio.

Generic Reader: at-mouse (object)
Generic Writer: (setf at-mouse) (object)
Package

cytoscape.

Methods
Reader Method: at-mouse ((context-menu context-menu))
Writer Method: (setf at-mouse) ((context-menu context-menu))

draw menu at mouse position

Source

context-menu.lisp.

Target Slot

at-mouse.

Generic Reader: auto-ungrabify (object)
Generic Writer: (setf auto-ungrabify) (object)
Package

cytoscape.

Methods
Reader Method: auto-ungrabify ((cytoscape-widget cytoscape-widget))
Writer Method: (setf auto-ungrabify) ((cytoscape-widget cytoscape-widget))

Whether nodes should be ungrabified (not grabbable by user) by default (if true, overrides individual node state).

Source

cytoscape.lisp.

Target Slot

auto-ungrabify.

Generic Reader: auto-unselectify (object)
Generic Writer: (setf auto-unselectify) (object)
Package

cytoscape.

Methods
Reader Method: auto-unselectify ((cytoscape-widget cytoscape-widget))
Writer Method: (setf auto-unselectify) ((cytoscape-widget cytoscape-widget))

Whether nodes should be unselectified (immutable selection state) by default (if true, overrides individual element state).

Source

cytoscape.lisp.

Target Slot

auto-unselectify.

Generic Reader: autolock (object)
Generic Writer: (setf autolock) (object)
Package

cytoscape.

Methods
Reader Method: autolock ((cytoscape-widget cytoscape-widget))
Writer Method: (setf autolock) ((cytoscape-widget cytoscape-widget))

Whether nodes should be locked (not draggable at all) by default (if true, overrides individual node state).

Source

cytoscape.lisp.

Target Slot

autolock.

Generic Reader: avoid-overlap (object)
Generic Writer: (setf avoid-overlap) (object)
Package

cytoscape.

Methods
Reader Method: avoid-overlap ((avoid-overlap-slot avoid-overlap-slot))
Writer Method: (setf avoid-overlap) ((avoid-overlap-slot avoid-overlap-slot))

Prevents node overlap, may overflow boundingBox if not enough space

Source

common-slots.lisp.

Target Slot

avoid-overlap.

Generic Reader: avoid-overlap-padding (object)
Generic Writer: (setf avoid-overlap-padding) (object)
Package

cytoscape.

Methods
Reader Method: avoid-overlap-padding ((grid-layout grid-layout))
Writer Method: (setf avoid-overlap-padding) ((grid-layout grid-layout))

Extra spacing around nodes when avoidOverlap: true

Source

graph-layout.lisp.

Target Slot

avoid-overlap-padding.

Generic Reader: border-spacing (object)
Generic Writer: (setf border-spacing) (object)
Package

cytoscape.

Methods
Reader Method: border-spacing ((klay-layout klay-layout))
Writer Method: (setf border-spacing) ((klay-layout klay-layout))
Source

graph-layout.lisp.

Target Slot

border-spacing.

Generic Reader: bounding-box (object)
Generic Writer: (setf bounding-box) (object)
Package

cytoscape.

Methods
Reader Method: bounding-box ((bounding-box-slot bounding-box-slot))
Writer Method: (setf bounding-box) ((bounding-box-slot bounding-box-slot))

constrain layout bounds; { x1, y1, x2, y2 } or { x1, y1, w, h }

Source

common-slots.lisp.

Target Slot

bounding-box.

Generic Reader: box-selection-enabled (object)
Generic Writer: (setf box-selection-enabled) (object)
Package

cytoscape.

Methods
Reader Method: box-selection-enabled ((cytoscape-widget cytoscape-widget))
Writer Method: (setf box-selection-enabled) ((cytoscape-widget cytoscape-widget))

Whether box selection (i.e. drag a box overlay around, and
release it to select) is enabled. If enabled while panning is also enabled, the user must use a modifier key (shift, alt, control, or command) to use box selection.

Source

cytoscape.lisp.

Target Slot

box-selection-enabled.

Generic Reader: circle (object)
Generic Writer: (setf circle) (object)
Package

cytoscape.

Methods
Reader Method: circle ((breadth-first-layout breadth-first-layout))
Writer Method: (setf circle) ((breadth-first-layout breadth-first-layout))

Put depths in concentric circles if true, put depths top down if false

Source

graph-layout.lisp.

Target Slot

circle.

Generic Reader: classes (object)
Generic Writer: (setf classes) (object)
Package

cytoscape.

Methods
Reader Method: classes ((element element))
Writer Method: (setf classes) ((element element))

A list of CSS classes

Source

cytoscape.lisp.

Target Slot

classes.

Generic Reader: clockwise (object)
Generic Writer: (setf clockwise) (object)
Package

cytoscape.

Methods
Reader Method: clockwise ((radial-slots radial-slots))
Writer Method: (setf clockwise) ((radial-slots radial-slots))

Whether the layout should go clockwise (true) or counterclockwise/anticlockwise (false)

Source

common-slots.lisp.

Target Slot

clockwise.

Generic Reader: cols (object)
Generic Writer: (setf cols) (object)
Package

cytoscape.

Methods
Reader Method: cols ((grid-layout grid-layout))
Writer Method: (setf cols) ((grid-layout grid-layout))

Force num of cols in the grid

Source

graph-layout.lisp.

Target Slot

cols.

Generic Reader: commands (object)
Generic Writer: (setf commands) (object)
Package

cytoscape.

Methods
Reader Method: commands ((context-menu context-menu))
Writer Method: (setf commands) ((context-menu context-menu))

an array of commands to list in the menu or a function that returns the array

Source

context-menu.lisp.

Target Slot

commands.

Generic Reader: compact-components (object)
Generic Writer: (setf compact-components) (object)
Package

cytoscape.

Methods
Reader Method: compact-components ((klay-layout klay-layout))
Writer Method: (setf compact-components) ((klay-layout klay-layout))
Source

graph-layout.lisp.

Target Slot

compact-components.

Generic Reader: component-spacing (object)
Generic Writer: (setf component-spacing) (object)
Package

cytoscape.

Methods
Reader Method: component-spacing ((cose-layout cose-layout))
Writer Method: (setf component-spacing) ((cose-layout cose-layout))

Extra spacing between components in non-compound graphs

Source

graph-layout.lisp.

Target Slot

component-spacing.

Generic Reader: condense (object)
Generic Writer: (setf condense) (object)
Package

cytoscape.

Methods
Reader Method: condense ((grid-layout grid-layout))
Writer Method: (setf condense) ((grid-layout grid-layout))

Uses all available space on false, uses minimal space on true

Source

graph-layout.lisp.

Target Slot

condense.

Generic Reader: content (object)
Generic Writer: (setf content) (object)
Package

cytoscape.

Methods
Reader Method: content ((menu-command menu-command))
Writer Method: (setf content) ((menu-command menu-command))

HTML/text content to be displayed in the menu.

Source

context-menu.lisp.

Target Slot

content.

Generic Reader: content-style (object)
Generic Writer: (setf content-style) (object)
Package

cytoscape.

Methods
Reader Method: content-style ((menu-command menu-command))
Writer Method: (setf content-style) ((menu-command menu-command))

css key:value pairs to set the command’s css in js if you want.

Source

context-menu.lisp.

Target Slot

content-style.

Generic Reader: context-menus (object)
Generic Writer: (setf context-menus) (object)
Package

cytoscape.

Methods
Reader Method: context-menus ((cytoscape-widget cytoscape-widget))
Writer Method: (setf context-menus) ((cytoscape-widget cytoscape-widget))

The context menus for the graph

Source

cytoscape.lisp.

Target Slot

context-menus.

Generic Reader: convergence-threshold (object)
Generic Writer: (setf convergence-threshold) (object)
Package

cytoscape.

Methods
Reader Method: convergence-threshold ((cola-layout cola-layout))
Writer Method: (setf convergence-threshold) ((cola-layout cola-layout))

When the alpha value (system energy) falls below this value, the layout stops

Source

graph-layout.lisp.

Target Slot

convergence-threshold.

Generic Reader: cooling-factor (object)
Generic Writer: (setf cooling-factor) (object)
Package

cytoscape.

Methods
Reader Method: cooling-factor ((cose-layout cose-layout))
Writer Method: (setf cooling-factor) ((cose-layout cose-layout))

Cooling factor (how the temperature is reduced between consecutive iterations

Source

graph-layout.lisp.

Target Slot

cooling-factor.

Generic Reader: crossing-minimization (object)
Generic Writer: (setf crossing-minimization) (object)
Package

cytoscape.

Methods
Reader Method: crossing-minimization ((klay-layout klay-layout))
Writer Method: (setf crossing-minimization) ((klay-layout klay-layout))
Source

graph-layout.lisp.

Target Slot

crossing-minimization.

Generic Reader: data (object)
Generic Writer: (setf data) (object)
Package

cytoscape.

Methods
Reader Method: data ((element element))
Writer Method: (setf data) ((element element))

An alist of the properties of the element.

Source

cytoscape.lisp.

Target Slot

data.

Generic Reader: desktop-tap-threshold (object)
Generic Writer: (setf desktop-tap-threshold) (object)
Package

cytoscape.

Methods
Reader Method: desktop-tap-threshold ((cytoscape-widget cytoscape-widget))
Writer Method: (setf desktop-tap-threshold) ((cytoscape-widget cytoscape-widget))

A non-negative integer that indicates the maximum allowable distance that a user may move during a tap gesture

Source

cytoscape.lisp.

Target Slot

desktop-tap-threshold.

Generic Reader: directed (object)
Generic Writer: (setf directed) (object)
Package

cytoscape.

Methods
Reader Method: directed ((breadth-first-layout breadth-first-layout))
Writer Method: (setf directed) ((breadth-first-layout breadth-first-layout))

Whether the tree is directed downwards (or edges can point in any direction if false)

Source

graph-layout.lisp.

Target Slot

directed.

Generic Reader: direction (object)
Generic Writer: (setf direction) (object)
Package

cytoscape.

Methods
Reader Method: direction ((klay-layout klay-layout))
Writer Method: (setf direction) ((klay-layout klay-layout))

UNDEFINED

Source

graph-layout.lisp.

Target Slot

direction.

Generic Reader: edge-elasticity (object)
Generic Writer: (setf edge-elasticity) (object)
Package

cytoscape.

Methods
Reader Method: edge-elasticity ((fcose-layout fcose-layout))
Writer Method: (setf edge-elasticity) ((fcose-layout fcose-layout))

Divisor to compute edge forces

Source

graph-layout.lisp.

Target Slot

edge-elasticity.

Reader Method: edge-elasticity ((cose-layout cose-layout))
Writer Method: (setf edge-elasticity) ((cose-layout cose-layout))

Divisor to compute edge forces. Can also be set per edge via data.

Source

graph-layout.lisp.

Target Slot

edge-elasticity.

Generic Reader: edge-jaccard-length (object)
Generic Writer: (setf edge-jaccard-length) (object)
Package

cytoscape.

Methods
Reader Method: edge-jaccard-length ((cola-layout cola-layout))
Writer Method: (setf edge-jaccard-length) ((cola-layout cola-layout))

Jaccard edge length in simulation. Can also be specified per edge via data.

Source

graph-layout.lisp.

Target Slot

edge-jaccard-length.

Generic Reader: edge-length (object)
Generic Writer: (setf edge-length) (object)
Package

cytoscape.

Methods
Reader Method: edge-length ((cola-layout cola-layout))
Writer Method: (setf edge-length) ((cola-layout cola-layout))

Sets edge length directly in simulation. Can also be specified per edge via data.

Source

graph-layout.lisp.

Target Slot

edge-length.

Generic Reader: edge-routing (object)
Generic Writer: (setf edge-routing) (object)
Package

cytoscape.

Methods
Reader Method: edge-routing ((klay-layout klay-layout))
Writer Method: (setf edge-routing) ((klay-layout klay-layout))
Source

graph-layout.lisp.

Target Slot

edge-routing.

Generic Reader: edge-sep (object)
Generic Writer: (setf edge-sep) (object)
Package

cytoscape.

Methods
Reader Method: edge-sep ((dagre-layout dagre-layout))
Writer Method: (setf edge-sep) ((dagre-layout dagre-layout))

the separation between adjacent edges in the same rank

Source

graph-layout.lisp.

Target Slot

edge-sep.

Generic Reader: edge-spacing-factor (object)
Generic Writer: (setf edge-spacing-factor) (object)
Package

cytoscape.

Methods
Reader Method: edge-spacing-factor ((klay-layout klay-layout))
Writer Method: (setf edge-spacing-factor) ((klay-layout klay-layout))
Source

graph-layout.lisp.

Target Slot

edge-spacing-factor.

Generic Reader: edge-sym-diff-length (object)
Generic Writer: (setf edge-sym-diff-length) (object)
Package

cytoscape.

Methods
Reader Method: edge-sym-diff-length ((cola-layout cola-layout))
Writer Method: (setf edge-sym-diff-length) ((cola-layout cola-layout))

Symmetric diff edge length in simulation. Can also be specified per edge via data.

Source

graph-layout.lisp.

Target Slot

edge-sym-diff-length.

Generic Reader: edge-weight (object)
Generic Writer: (setf edge-weight) (object)
Package

cytoscape.

Methods
Reader Method: edge-weight ((dagre-layout dagre-layout))
Writer Method: (setf edge-weight) ((dagre-layout dagre-layout))

Higher weight edges are generally made shorter and straighter than lower weight edges. Can also be set per edge via data.

Source

graph-layout.lisp.

Target Slot

edge-weight.

Generic Reader: elements (object)
Generic Writer: (setf elements) (object)
Package

cytoscape.

Methods
Reader Method: elements ((cytoscape-widget cytoscape-widget))
Writer Method: (setf elements) ((cytoscape-widget cytoscape-widget))

The list of graph elements

Source

cytoscape.lisp.

Target Slot

elements.

Generic Reader: enabled (object)
Generic Writer: (setf enabled) (object)
Package

cytoscape.

Methods
Reader Method: enabled ((menu-command menu-command))
Writer Method: (setf enabled) ((menu-command menu-command))

Whether the command is selectable.

Source

context-menu.lisp.

Target Slot

enabled.

Generic Reader: equidistant (object)
Generic Writer: (setf equidistant) (object)
Package

cytoscape.

Methods
Reader Method: equidistant ((concentric-layout concentric-layout))
Writer Method: (setf equidistant) ((concentric-layout concentric-layout))

Whether levels have an equal radial distance betwen them, may cause bounding box overflow

Source

graph-layout.lisp.

Target Slot

equidistant.

Generic Reader: feedback-edges (object)
Generic Writer: (setf feedback-edges) (object)
Package

cytoscape.

Methods
Reader Method: feedback-edges ((klay-layout klay-layout))
Writer Method: (setf feedback-edges) ((klay-layout klay-layout))
Source

graph-layout.lisp.

Target Slot

feedback-edges.

Generic Reader: fill-color (object)
Generic Writer: (setf fill-color) (object)
Package

cytoscape.

Methods
Reader Method: fill-color ((context-menu context-menu))
Writer Method: (setf fill-color) ((context-menu context-menu))

the background colour of the menu

Source

context-menu.lisp.

Target Slot

fill-color.

Reader Method: fill-color ((menu-command menu-command))
Writer Method: (setf fill-color) ((menu-command menu-command))

Custom background color for item.

Source

context-menu.lisp.

Target Slot

fill-color.

Generic Reader: fit (object)
Generic Writer: (setf fit) (object)
Package

cytoscape.

Methods
Reader Method: fit ((common-slots common-slots))
Writer Method: (setf fit) ((common-slots common-slots))

Whether to fit the viewport to the graph

Source

common-slots.lisp.

Target Slot

fit.

Generic Reader: fixed-alignment (object)
Generic Writer: (setf fixed-alignment) (object)
Package

cytoscape.

Methods
Reader Method: fixed-alignment ((klay-layout klay-layout))
Writer Method: (setf fixed-alignment) ((klay-layout klay-layout))
Source

graph-layout.lisp.

Target Slot

fixed-alignment.

Generic Reader: flow (object)
Generic Writer: (setf flow) (object)
Package

cytoscape.

Methods
Reader Method: flow ((cola-layout cola-layout))
Writer Method: (setf flow) ((cola-layout cola-layout))

use DAG/tree flow layout if specified, e.g. { axis: ’y’, minSeparation: 30 }

Source

graph-layout.lisp.

Target Slot

flow.

Generic Reader: gap-inequalities (object)
Generic Writer: (setf gap-inequalities) (object)
Package

cytoscape.

Methods
Reader Method: gap-inequalities ((cola-layout cola-layout))
Writer Method: (setf gap-inequalities) ((cola-layout cola-layout))

list of inequality constraints for the gap between the nodes, e.g. [{"axis":"y", "left":node1, "right":node2, "gap":25}]

Source

graph-layout.lisp.

Target Slot

gap-inequalities.

Generic Reader: grabbable (object)
Generic Writer: (setf grabbable) (object)
Package

cytoscape.

Methods
Reader Method: grabbable ((element element))
Writer Method: (setf grabbable) ((element element))

T if the element can be grabbed.

Source

cytoscape.lisp.

Target Slot

grabbable.

Generic Reader: grabbed (object)
Generic Writer: (setf grabbed) (object)
Package

cytoscape.

Methods
Reader Method: grabbed ((element element))
Writer Method: (setf grabbed) ((element element))

T if if the element is currently grabbed.

Source

cytoscape.lisp.

Target Slot

grabbed.

Generic Reader: graph-layouts (object)
Generic Writer: (setf graph-layouts) (object)
Package

cytoscape.

Methods
Reader Method: graph-layouts ((cytoscape-widget cytoscape-widget))
Writer Method: (setf graph-layouts) ((cytoscape-widget cytoscape-widget))

Layout algorithms

Source

cytoscape.lisp.

Target Slot

graph-layouts.

Generic Reader: graph-style (object)
Generic Writer: (setf graph-style) (object)
Package

cytoscape.

Methods
Reader Method: graph-style ((cytoscape-widget cytoscape-widget))
Writer Method: (setf graph-style) ((cytoscape-widget cytoscape-widget))

The stylesheet for the graph

Source

cytoscape.lisp.

Target Slot

graph-style.

Generic Reader: gravity (object)
Generic Writer: (setf gravity) (object)
Package

cytoscape.

Methods
Reader Method: gravity ((gravity-slot gravity-slot))
Writer Method: (setf gravity) ((gravity-slot gravity-slot))

Gravity force (constant)

Source

common-slots.lisp.

Target Slot

gravity.

Generic Reader: gravity-compound (object)
Generic Writer: (setf gravity-compound) (object)
Package

cytoscape.

Methods
Reader Method: gravity-compound ((fcose-layout fcose-layout))
Writer Method: (setf gravity-compound) ((fcose-layout fcose-layout))

Gravity force (constant) for compounds

Source

graph-layout.lisp.

Target Slot

gravity-compound.

Generic Reader: gravity-range (object)
Generic Writer: (setf gravity-range) (object)
Package

cytoscape.

Methods
Reader Method: gravity-range ((fcose-layout fcose-layout))
Writer Method: (setf gravity-range) ((fcose-layout fcose-layout))

Gravity range (constant)

Source

graph-layout.lisp.

Target Slot

gravity-range.

Generic Reader: gravity-range-compound (object)
Generic Writer: (setf gravity-range-compound) (object)
Package

cytoscape.

Methods
Reader Method: gravity-range-compound ((fcose-layout fcose-layout))
Writer Method: (setf gravity-range-compound) ((fcose-layout fcose-layout))

Gravity range (constant) for compounds

Source

graph-layout.lisp.

Target Slot

gravity-range-compound.

Generic Reader: grid (object)
Generic Writer: (setf grid) (object)
Package

cytoscape.

Methods
Reader Method: grid ((breadth-first-layout breadth-first-layout))
Writer Method: (setf grid) ((breadth-first-layout breadth-first-layout))

Whether to create an even grid into which the DAG is placed (circle:false only)

Source

graph-layout.lisp.

Target Slot

grid.

Generic Reader: group (object)
Generic Writer: (setf group) (object)
Package

cytoscape.

Methods
Reader Method: group ((element element))
Writer Method: (setf group) ((element element))

Element type. Must be either nodes or edges.

Source

cytoscape.lisp.

Target Slot

group.

Generic Reader: handle-disconnected (object)
Generic Writer: (setf handle-disconnected) (object)
Package

cytoscape.

Methods
Reader Method: handle-disconnected ((cola-layout cola-layout))
Writer Method: (setf handle-disconnected) ((cola-layout cola-layout))

if true, avoids disconnected components from overlapping

Source

graph-layout.lisp.

Target Slot

handle-disconnected.

Generic Reader: headless (object)
Generic Writer: (setf headless) (object)
Package

cytoscape.

Methods
Reader Method: headless ((cytoscape-widget cytoscape-widget))
Writer Method: (setf headless) ((cytoscape-widget cytoscape-widget))

A convenience option that initialises the instance to run headlessly.

Source

cytoscape.lisp.

Target Slot

headless.

Generic Reader: hide-edges-on-viewport (object)
Generic Writer: (setf hide-edges-on-viewport) (object)
Package

cytoscape.

Methods
Reader Method: hide-edges-on-viewport ((cytoscape-widget cytoscape-widget))
Writer Method: (setf hide-edges-on-viewport) ((cytoscape-widget cytoscape-widget))

A rendering hint that when set to t makes the renderer
not render edges while the viewport is being manipulated. This makes panning, zooming, dragging, et cetera more responsive for large graphs.

Source

cytoscape.lisp.

Target Slot

hide-edges-on-viewport.

Generic Reader: ideal-edge-length (object)
Generic Writer: (setf ideal-edge-length) (object)
Package

cytoscape.

Methods
Reader Method: ideal-edge-length ((fcose-layout fcose-layout))
Writer Method: (setf ideal-edge-length) ((fcose-layout fcose-layout))

Ideal edge (non nested) length

Source

graph-layout.lisp.

Target Slot

ideal-edge-length.

Reader Method: ideal-edge-length ((cose-layout cose-layout))
Writer Method: (setf ideal-edge-length) ((cose-layout cose-layout))

Ideal edge (non nested) length. Can also be set per edge via data.

Source

graph-layout.lisp.

Target Slot

ideal-edge-length.

Generic Reader: in-layer-spacing-factor (object)
Generic Writer: (setf in-layer-spacing-factor) (object)
Package

cytoscape.

Methods
Reader Method: in-layer-spacing-factor ((klay-layout klay-layout))
Writer Method: (setf in-layer-spacing-factor) ((klay-layout klay-layout))
Source

graph-layout.lisp.

Target Slot

in-layer-spacing-factor.

Generic Reader: indicator-size (object)
Generic Writer: (setf indicator-size) (object)
Package

cytoscape.

Methods
Reader Method: indicator-size ((context-menu context-menu))
Writer Method: (setf indicator-size) ((context-menu context-menu))

the size in pixels of the pointer to the active command

Source

context-menu.lisp.

Target Slot

indicator-size.

Generic Reader: initial-energy-on-incremental (object)
Generic Writer: (setf initial-energy-on-incremental) (object)
Package

cytoscape.

Methods
Reader Method: initial-energy-on-incremental ((fcose-layout fcose-layout))
Writer Method: (setf initial-energy-on-incremental) ((fcose-layout fcose-layout))

Initial cooling factor for incremental layout

Source

graph-layout.lisp.

Target Slot

initial-energy-on-incremental.

Generic Reader: initial-temp (object)
Generic Writer: (setf initial-temp) (object)
Package

cytoscape.

Methods
Reader Method: initial-temp ((cose-layout cose-layout))
Writer Method: (setf initial-temp) ((cose-layout cose-layout))

Initial temperature (maximum node displacement)

Source

graph-layout.lisp.

Target Slot

initial-temp.

Generic Reader: item-color (object)
Generic Writer: (setf item-color) (object)
Package

cytoscape.

Methods
Reader Method: item-color ((context-menu context-menu))
Writer Method: (setf item-color) ((context-menu context-menu))

the colour of text in the command’s content

Source

context-menu.lisp.

Target Slot

item-color.

Generic Reader: item-text-shadow-color (object)
Generic Writer: (setf item-text-shadow-color) (object)
Package

cytoscape.

Methods
Reader Method: item-text-shadow-color ((context-menu context-menu))
Writer Method: (setf item-text-shadow-color) ((context-menu context-menu))

the text shadow colour of the command’s content

Source

context-menu.lisp.

Target Slot

item-text-shadow-color.

Generic Reader: layout-hierarchy (object)
Generic Writer: (setf layout-hierarchy) (object)
Package

cytoscape.

Methods
Reader Method: layout-hierarchy ((klay-layout klay-layout))
Writer Method: (setf layout-hierarchy) ((klay-layout klay-layout))
Source

graph-layout.lisp.

Target Slot

layout-hierarchy.

Generic Reader: linear-segments-deflection-dampening (object)
Generic Writer: (setf linear-segments-deflection-dampening) (object)
Package

cytoscape.

Methods
Reader Method: linear-segments-deflection-dampening ((klay-layout klay-layout))
Writer Method: (setf linear-segments-deflection-dampening) ((klay-layout klay-layout))
Source

graph-layout.lisp.

Target Slot

linear-segments-deflection-dampening.

Generic Reader: locked (object)
Generic Writer: (setf locked) (object)
Package

cytoscape.

Methods
Reader Method: locked ((element element))
Writer Method: (setf locked) ((element element))

T if the element will not be moved during a layout.

Source

cytoscape.lisp.

Target Slot

locked.

Generic Reader: max-simulation-time (object)
Generic Writer: (setf max-simulation-time) (object)
Package

cytoscape.

Methods
Reader Method: max-simulation-time ((cola-layout cola-layout))
Writer Method: (setf max-simulation-time) ((cola-layout cola-layout))

max length in ms to run the layout

Source

graph-layout.lisp.

Target Slot

max-simulation-time.

Generic Reader: max-spotlight-radius (object)
Generic Writer: (setf max-spotlight-radius) (object)
Package

cytoscape.

Methods
Reader Method: max-spotlight-radius ((context-menu context-menu))
Writer Method: (setf max-spotlight-radius) ((context-menu context-menu))

the maximum radius in pixels of the spotlight

Source

context-menu.lisp.

Target Slot

max-spotlight-radius.

Generic Reader: max-zoom (object)
Generic Writer: (setf max-zoom) (object)
Package

cytoscape.

Methods
Reader Method: max-zoom ((cytoscape-widget cytoscape-widget))
Writer Method: (setf max-zoom) ((cytoscape-widget cytoscape-widget))

A maximum bound on the zoom level of the graph. The viewport can not be scaled larger than this zoom level.

Source

cytoscape.lisp.

Target Slot

max-zoom.

Generic Reader: maximal (object)
Generic Writer: (setf maximal) (object)
Package

cytoscape.

Methods
Reader Method: maximal ((breadth-first-layout breadth-first-layout))
Writer Method: (setf maximal) ((breadth-first-layout breadth-first-layout))

Whether to shift nodes down their natural BFS depths in order to avoid upwards edges (DAGS only)

Source

graph-layout.lisp.

Target Slot

maximal.

Generic Reader: menu-radius (object)
Generic Writer: (setf menu-radius) (object)
Package

cytoscape.

Methods
Reader Method: menu-radius ((context-menu context-menu))
Writer Method: (setf menu-radius) ((context-menu context-menu))

the radius of the circular menu in pixels

Source

context-menu.lisp.

Target Slot

menu-radius.

Generic Reader: merge-edges (object)
Generic Writer: (setf merge-edges) (object)
Package

cytoscape.

Methods
Reader Method: merge-edges ((klay-layout klay-layout))
Writer Method: (setf merge-edges) ((klay-layout klay-layout))
Source

graph-layout.lisp.

Target Slot

merge-edges.

Generic Reader: merge-hierarchy-crossing-edges (object)
Generic Writer: (setf merge-hierarchy-crossing-edges) (object)
Package

cytoscape.

Methods
Reader Method: merge-hierarchy-crossing-edges ((klay-layout klay-layout))
Writer Method: (setf merge-hierarchy-crossing-edges) ((klay-layout klay-layout))
Source

graph-layout.lisp.

Target Slot

merge-hierarchy-crossing-edges.

Generic Reader: min-length (object)
Generic Writer: (setf min-length) (object)
Package

cytoscape.

Methods
Reader Method: min-length ((dagre-layout dagre-layout))
Writer Method: (setf min-length) ((dagre-layout dagre-layout))

Number of ranks to keep between the source and target of the edge. Can also be set per edge via data.

Source

graph-layout.lisp.

Target Slot

min-length.

Generic Reader: min-node-spacing (object)
Generic Writer: (setf min-node-spacing) (object)
Package

cytoscape.

Methods
Reader Method: min-node-spacing ((concentric-layout concentric-layout))
Writer Method: (setf min-node-spacing) ((concentric-layout concentric-layout))

Min spacing between outside of nodes (used for radius adjustment)

Source

graph-layout.lisp.

Target Slot

min-node-spacing.

Generic Reader: min-spotlight-radius (object)
Generic Writer: (setf min-spotlight-radius) (object)
Package

cytoscape.

Methods
Reader Method: min-spotlight-radius ((context-menu context-menu))
Writer Method: (setf min-spotlight-radius) ((context-menu context-menu))

the minimum radius in pixels of the spotlight

Source

context-menu.lisp.

Target Slot

min-spotlight-radius.

Generic Reader: min-temp (object)
Generic Writer: (setf min-temp) (object)
Package

cytoscape.

Methods
Reader Method: min-temp ((cose-layout cose-layout))
Writer Method: (setf min-temp) ((cose-layout cose-layout))

Lower temperature threshold (below this point the layout will end)

Source

graph-layout.lisp.

Target Slot

min-temp.

Generic Reader: min-zoom (object)
Generic Writer: (setf min-zoom) (object)
Package

cytoscape.

Methods
Reader Method: min-zoom ((cytoscape-widget cytoscape-widget))
Writer Method: (setf min-zoom) ((cytoscape-widget cytoscape-widget))

A minimum bound on the zoom level of the graph. The viewport can not be scaled smaller than this zoom level.

Source

cytoscape.lisp.

Target Slot

min-zoom.

Generic Reader: motion-blur (object)
Generic Writer: (setf motion-blur) (object)
Package

cytoscape.

Methods
Reader Method: motion-blur ((cytoscape-widget cytoscape-widget))
Writer Method: (setf motion-blur) ((cytoscape-widget cytoscape-widget))

A rendering hint that when set to t makes the renderer
use a motion blur effect to make the transition between frames seem smoother.

Source

cytoscape.lisp.

Target Slot

motion-blur.

Generic Reader: motion-blur-opacity (object)
Generic Writer: (setf motion-blur-opacity) (object)
Package

cytoscape.

Methods
Reader Method: motion-blur-opacity ((cytoscape-widget cytoscape-widget))
Writer Method: (setf motion-blur-opacity) ((cytoscape-widget cytoscape-widget))

When motionBlur: t, this value controls the opacity of motion blur frames.

Source

cytoscape.lisp.

Target Slot

motion-blur-opacity.

Generic Reader: nesting-factor (object)
Generic Writer: (setf nesting-factor) (object)
Package

cytoscape.

Methods
Reader Method: nesting-factor ((nesting-factor-slot nesting-factor-slot))
Writer Method: (setf nesting-factor) ((nesting-factor-slot nesting-factor-slot))

Nesting factor (multiplier) to compute ideal edge length for nested edges

Source

common-slots.lisp.

Target Slot

nesting-factor.

Generic Reader: node-dimensions-include-labels (object)
Generic Writer: (setf node-dimensions-include-labels) (object)
Package

cytoscape.

Methods
Reader Method: node-dimensions-include-labels ((node-dimensions-include-labels-slot node-dimensions-include-labels-slot))
Writer Method: (setf node-dimensions-include-labels) ((node-dimensions-include-labels-slot node-dimensions-include-labels-slot))

Includes the label when calculating node bounding boxes for the layout algorithm.

Source

common-slots.lisp.

Target Slot

node-dimensions-include-labels.

Generic Reader: node-layering (object)
Generic Writer: (setf node-layering) (object)
Package

cytoscape.

Methods
Reader Method: node-layering ((klay-layout klay-layout))
Writer Method: (setf node-layering) ((klay-layout klay-layout))
Source

graph-layout.lisp.

Target Slot

node-layering.

Generic Reader: node-overlap (object)
Generic Writer: (setf node-overlap) (object)
Package

cytoscape.

Methods
Reader Method: node-overlap ((cose-layout cose-layout))
Writer Method: (setf node-overlap) ((cose-layout cose-layout))

Node repulsion (overlapping) multiplier

Source

graph-layout.lisp.

Target Slot

node-overlap.

Generic Reader: node-placement (object)
Generic Writer: (setf node-placement) (object)
Package

cytoscape.

Methods
Reader Method: node-placement ((klay-layout klay-layout))
Writer Method: (setf node-placement) ((klay-layout klay-layout))
Source

graph-layout.lisp.

Target Slot

node-placement.

Generic Reader: node-repulsion (object)
Generic Writer: (setf node-repulsion) (object)
Package

cytoscape.

Methods
Reader Method: node-repulsion ((fcose-layout fcose-layout))
Writer Method: (setf node-repulsion) ((fcose-layout fcose-layout))

Node repulsion (non overlapping) multiplier

Source

graph-layout.lisp.

Target Slot

node-repulsion.

Reader Method: node-repulsion ((cose-layout cose-layout))
Writer Method: (setf node-repulsion) ((cose-layout cose-layout))

Node repulsion (non overlapping) multiplier. Can also be set per node in data.

Source

graph-layout.lisp.

Target Slot

node-repulsion.

Generic Reader: node-sep (object)
Generic Writer: (setf node-sep) (object)
Package

cytoscape.

Methods
Reader Method: node-sep ((dagre-layout dagre-layout))
Writer Method: (setf node-sep) ((dagre-layout dagre-layout))

the separation between adjacent nodes in the same rank

Source

graph-layout.lisp.

Target Slot

node-sep.

Generic Reader: node-separation (object)
Generic Writer: (setf node-separation) (object)
Package

cytoscape.

Methods
Reader Method: node-separation ((fcose-layout fcose-layout))
Writer Method: (setf node-separation) ((fcose-layout fcose-layout))

Separation amount between nodes

Source

graph-layout.lisp.

Target Slot

node-separation.

Generic Reader: num-iter (object)
Generic Writer: (setf num-iter) (object)
Package

cytoscape.

Methods
Reader Method: num-iter ((num-iter-slot num-iter-slot))
Writer Method: (setf num-iter) ((num-iter-slot num-iter-slot))

Maximum number of iterations to perform

Source

common-slots.lisp.

Target Slot

num-iter.

Generic Reader: pack-components (object)
Generic Writer: (setf pack-components) (object)
Package

cytoscape.

Methods
Reader Method: pack-components ((fcose-layout fcose-layout))
Writer Method: (setf pack-components) ((fcose-layout fcose-layout))

Whether to pack disconnected components - valid only if randomize: true

Source

graph-layout.lisp.

Target Slot

pack-components.

Generic Reader: padding (object)
Generic Writer: (setf padding) (object)
Package

cytoscape.

Methods
Reader Method: padding ((common-slots common-slots))
Writer Method: (setf padding) ((common-slots common-slots))

Padding to leave between graph and viewport

Source

common-slots.lisp.

Target Slot

padding.

Generic Reader: pan (object)
Generic Writer: (setf pan) (object)
Package

cytoscape.

Methods
Reader Method: pan ((cytoscape-widget cytoscape-widget))
Writer Method: (setf pan) ((cytoscape-widget cytoscape-widget))

Pan location of the graph.

Source

cytoscape.lisp.

Target Slot

pan.

Reader Method: pan ((preset-layout preset-layout))
Writer Method: (setf pan) ((preset-layout preset-layout))

The pan level to set (prob want fit = false if set)

Source

graph-layout.lisp.

Target Slot

pan.

Generic Reader: panning-enabled (object)
Generic Writer: (setf panning-enabled) (object)
Package

cytoscape.

Methods
Reader Method: panning-enabled ((cytoscape-widget cytoscape-widget))
Writer Method: (setf panning-enabled) ((cytoscape-widget cytoscape-widget))

Whether panning the graph is enabled, both by user events sand programmatically.

Source

cytoscape.lisp.

Target Slot

panning-enabled.

Generic Reader: pi-tol (object)
Generic Writer: (setf pi-tol) (object)
Package

cytoscape.

Methods
Reader Method: pi-tol ((fcose-layout fcose-layout))
Writer Method: (setf pi-tol) ((fcose-layout fcose-layout))

Power iteration tolerance

Source

graph-layout.lisp.

Target Slot

pi-tol.

Generic Reader: quality (object)
Generic Writer: (setf quality) (object)
Package

cytoscape.

Methods
Reader Method: quality ((fcose-layout fcose-layout))
Writer Method: (setf quality) ((fcose-layout fcose-layout))

Layout quality

Source

graph-layout.lisp.

Target Slot

quality.

Generic Reader: radius (object)
Generic Writer: (setf radius) (object)
Package

cytoscape.

Methods
Reader Method: radius ((circle-layout circle-layout))
Writer Method: (setf radius) ((circle-layout circle-layout))

The radius of the circle

Source

graph-layout.lisp.

Target Slot

radius.

Generic Reader: randomization-seed (object)
Generic Writer: (setf randomization-seed) (object)
Package

cytoscape.

Methods
Reader Method: randomization-seed ((klay-layout klay-layout))
Writer Method: (setf randomization-seed) ((klay-layout klay-layout))
Source

graph-layout.lisp.

Target Slot

randomization-seed.

Generic Reader: randomize (object)
Generic Writer: (setf randomize) (object)
Package

cytoscape.

Methods
Reader Method: randomize ((randomize-slot randomize-slot))
Writer Method: (setf randomize) ((randomize-slot randomize-slot))

Use random node positions at beginning of layout

Source

common-slots.lisp.

Target Slot

randomize.

Generic Reader: rank-dir (object)
Generic Writer: (setf rank-dir) (object)
Package

cytoscape.

Methods
Reader Method: rank-dir ((dagre-layout dagre-layout))
Writer Method: (setf rank-dir) ((dagre-layout dagre-layout))

’TB’ for top to bottom flow, ’LR’ for left to right,

Source

graph-layout.lisp.

Target Slot

rank-dir.

Generic Reader: rank-sep (object)
Generic Writer: (setf rank-sep) (object)
Package

cytoscape.

Methods
Reader Method: rank-sep ((dagre-layout dagre-layout))
Writer Method: (setf rank-sep) ((dagre-layout dagre-layout))

the separation between each rank in the layout

Source

graph-layout.lisp.

Target Slot

rank-sep.

Generic Reader: ranker (object)
Generic Writer: (setf ranker) (object)
Package

cytoscape.

Methods
Reader Method: ranker ((dagre-layout dagre-layout))
Writer Method: (setf ranker) ((dagre-layout dagre-layout))

Type of algorithm to assign a rank to each node in the input graph. Possible values: ’network-simplex’, ’tight-tree’ or ’longest-path’

Source

graph-layout.lisp.

Target Slot

ranker.

Generic Reader: refresh (object)
Generic Writer: (setf refresh) (object)
Package

cytoscape.

Methods
Reader Method: refresh ((refresh-slot refresh-slot))
Writer Method: (setf refresh) ((refresh-slot refresh-slot))

Number of ticks per frame; higher is faster but more jerky

Source

common-slots.lisp.

Target Slot

refresh.

Generic Reader: removed (object)
Generic Writer: (setf removed) (object)
Package

cytoscape.

Methods
Reader Method: removed ((element element))
Writer Method: (setf removed) ((element element))

T if the element has been removed from the graph.

Source

cytoscape.lisp.

Target Slot

removed.

Generic Reader: roots (object)
Generic Writer: (setf roots) (object)
Package

cytoscape.

Methods
Reader Method: roots ((breadth-first-layout breadth-first-layout))
Writer Method: (setf roots) ((breadth-first-layout breadth-first-layout))

The roots of the trees

Source

graph-layout.lisp.

Target Slot

roots.

Generic Reader: route-self-loop-inside (object)
Generic Writer: (setf route-self-loop-inside) (object)
Package

cytoscape.

Methods
Reader Method: route-self-loop-inside ((klay-layout klay-layout))
Writer Method: (setf route-self-loop-inside) ((klay-layout klay-layout))
Source

graph-layout.lisp.

Target Slot

route-self-loop-inside.

Generic Reader: rows (object)
Generic Writer: (setf rows) (object)
Package

cytoscape.

Methods
Reader Method: rows ((grid-layout grid-layout))
Writer Method: (setf rows) ((grid-layout grid-layout))

Force num of rows in the grid

Source

graph-layout.lisp.

Target Slot

rows.

Generic Reader: sample-size (object)
Generic Writer: (setf sample-size) (object)
Package

cytoscape.

Methods
Reader Method: sample-size ((fcose-layout fcose-layout))
Writer Method: (setf sample-size) ((fcose-layout fcose-layout))

Sample size to construct distance matrix

Source

graph-layout.lisp.

Target Slot

sample-size.

Generic Reader: sampling-type (object)
Generic Writer: (setf sampling-type) (object)
Package

cytoscape.

Methods
Reader Method: sampling-type ((fcose-layout fcose-layout))
Writer Method: (setf sampling-type) ((fcose-layout fcose-layout))

False for random, true for greedy sampling

Source

graph-layout.lisp.

Target Slot

sampling-type.

Generic Reader: selectable (object)
Generic Writer: (setf selectable) (object)
Package

cytoscape.

Methods
Reader Method: selectable ((element element))
Writer Method: (setf selectable) ((element element))

T if the element can be selected.

Source

cytoscape.lisp.

Target Slot

selectable.

Generic Reader: selected (object)
Generic Writer: (setf selected) (object)
Package

cytoscape.

Methods
Reader Method: selected ((element element))
Writer Method: (setf selected) ((element element))

Whether the element is selected in the graph.

Source

cytoscape.lisp.

Target Slot

selected.

Generic Reader: selection-type (object)
Generic Writer: (setf selection-type) (object)
Package

cytoscape.

Methods
Reader Method: selection-type ((cytoscape-widget cytoscape-widget))
Writer Method: (setf selection-type) ((cytoscape-widget cytoscape-widget))

A string indicating the selection behaviour from user input.
For ’additive’, a new selection made by the user adds to the set of currently selected elements. For ’single’, a new selection made by the user becomes the entire set of currently selected elements (i.e. the previous elements are unselected).

Source

cytoscape.lisp.

Target Slot

selection-type.

Generic Reader: selector (object)
Generic Writer: (setf selector) (object)
Package

cytoscape.

Methods
Reader Method: selector ((graph-layout graph-layout))
Writer Method: (setf selector) ((graph-layout graph-layout))

Elements that the layout applies to.

Source

graph-layout.lisp.

Target Slot

selector.

Reader Method: selector ((context-menu context-menu))
Writer Method: (setf selector) ((context-menu context-menu))

Elements matching this Cytoscape.js selector will trigger this menu

Source

context-menu.lisp.

Target Slot

selector.

Generic Reader: separate-connected-components (object)
Generic Writer: (setf separate-connected-components) (object)
Package

cytoscape.

Methods
Reader Method: separate-connected-components ((klay-layout klay-layout))
Writer Method: (setf separate-connected-components) ((klay-layout klay-layout))
Source

graph-layout.lisp.

Target Slot

separate-connected-components.

Generic Reader: separator-width (object)
Generic Writer: (setf separator-width) (object)
Package

cytoscape.

Methods
Reader Method: separator-width ((context-menu context-menu))
Writer Method: (setf separator-width) ((context-menu context-menu))

the empty spacing in pixels between successive commands

Source

context-menu.lisp.

Target Slot

separator-width.

Generic Reader: spacing (object)
Generic Writer: (setf spacing) (object)
Package

cytoscape.

Methods
Reader Method: spacing ((klay-layout klay-layout))
Writer Method: (setf spacing) ((klay-layout klay-layout))
Source

graph-layout.lisp.

Target Slot

spacing.

Generic Reader: spacing-factor (object)
Generic Writer: (setf spacing-factor) (object)
Package

cytoscape.

Methods
Reader Method: spacing-factor ((spacing-factor-slot spacing-factor-slot))
Writer Method: (setf spacing-factor) ((spacing-factor-slot spacing-factor-slot))

Applies a multiplicative factor (>0) to expand or compress the overall area that the nodes take up

Source

common-slots.lisp.

Target Slot

spacing-factor.

Generic Reader: spotlight-padding (object)
Generic Writer: (setf spotlight-padding) (object)
Package

cytoscape.

Methods
Reader Method: spotlight-padding ((context-menu context-menu))
Writer Method: (setf spotlight-padding) ((context-menu context-menu))

extra spacing in pixels between the element and the spotlight

Source

context-menu.lisp.

Target Slot

spotlight-padding.

Generic Reader: start-angle (object)
Generic Writer: (setf start-angle) (object)
Package

cytoscape.

Methods
Reader Method: start-angle ((radial-slots radial-slots))
Writer Method: (setf start-angle) ((radial-slots radial-slots))

Where nodes start in radians

Source

common-slots.lisp.

Target Slot

start-angle.

Generic Reader: style-enabled (object)
Generic Writer: (setf style-enabled) (object)
Package

cytoscape.

Methods
Reader Method: style-enabled ((cytoscape-widget cytoscape-widget))
Writer Method: (setf style-enabled) ((cytoscape-widget cytoscape-widget))

A boolean that indicates whether styling should be used.
For headless (i.e. outside the browser) environments, display is not necessary and so neither is styling necessary — thereby speeding up your code.

Source

cytoscape.lisp.

Target Slot

style-enabled.

Generic Reader: sweep (object)
Generic Writer: (setf sweep) (object)
Package

cytoscape.

Methods
Reader Method: sweep ((radial-slots radial-slots))
Writer Method: (setf sweep) ((radial-slots radial-slots))

How many radians should be between the first and last node (defaults to full circle)

Source

common-slots.lisp.

Target Slot

sweep.

Generic Reader: texture-on-viewport (object)
Generic Writer: (setf texture-on-viewport) (object)
Package

cytoscape.

Methods
Reader Method: texture-on-viewport ((cytoscape-widget cytoscape-widget))
Writer Method: (setf texture-on-viewport) ((cytoscape-widget cytoscape-widget))

A rendering hint that when set to true makes the
renderer use a texture during panning and zooming instead of drawing the elements, making large graphs more responsive.

Source

cytoscape.lisp.

Target Slot

texture-on-viewport.

Generic Reader: thoroughness (object)
Generic Writer: (setf thoroughness) (object)
Package

cytoscape.

Methods
Reader Method: thoroughness ((klay-layout klay-layout))
Writer Method: (setf thoroughness) ((klay-layout klay-layout))
Source

graph-layout.lisp.

Target Slot

thoroughness.

Generic Reader: tile (object)
Generic Writer: (setf tile) (object)
Package

cytoscape.

Methods
Reader Method: tile ((fcose-layout fcose-layout))
Writer Method: (setf tile) ((fcose-layout fcose-layout))

For enabling tiling

Source

graph-layout.lisp.

Target Slot

tile.

Generic Reader: tile-padding-horizontal (object)
Generic Writer: (setf tile-padding-horizontal) (object)
Package

cytoscape.

Methods
Reader Method: tile-padding-horizontal ((fcose-layout fcose-layout))
Writer Method: (setf tile-padding-horizontal) ((fcose-layout fcose-layout))

Represents the amount of the horizontal space to put between the zero degree members during the tiling operation(can also be a function)

Source

graph-layout.lisp.

Target Slot

tile-padding-horizontal.

Generic Reader: tile-padding-vertical (object)
Generic Writer: (setf tile-padding-vertical) (object)
Package

cytoscape.

Methods
Reader Method: tile-padding-vertical ((fcose-layout fcose-layout))
Writer Method: (setf tile-padding-vertical) ((fcose-layout fcose-layout))

Represents the amount of the vertical space to put between the zero degree members during the tiling operation(can also be a function)

Source

graph-layout.lisp.

Target Slot

tile-padding-vertical.

Generic Reader: touch-tap-threshold (object)
Generic Writer: (setf touch-tap-threshold) (object)
Package

cytoscape.

Methods
Reader Method: touch-tap-threshold ((cytoscape-widget cytoscape-widget))
Writer Method: (setf touch-tap-threshold) ((cytoscape-widget cytoscape-widget))

A non-negative integer that indicates the maximum allowable distance that a user may move during a tap gesture

Source

cytoscape.lisp.

Target Slot

touch-tap-threshold.

Generic Reader: unconst-iter (object)
Generic Writer: (setf unconst-iter) (object)
Package

cytoscape.

Methods
Reader Method: unconst-iter ((cola-layout cola-layout))
Writer Method: (setf unconst-iter) ((cola-layout cola-layout))

unconstrained initial layout iterations

Source

graph-layout.lisp.

Target Slot

unconst-iter.

Generic Reader: ungrabify-while-simulating (object)
Generic Writer: (setf ungrabify-while-simulating) (object)
Package

cytoscape.

Methods
Reader Method: ungrabify-while-simulating ((cola-layout cola-layout))
Writer Method: (setf ungrabify-while-simulating) ((cola-layout cola-layout))

So you can’t drag nodes during layout

Source

graph-layout.lisp.

Target Slot

ungrabify-while-simulating.

Generic Reader: uniform-node-dimensions (object)
Generic Writer: (setf uniform-node-dimensions) (object)
Package

cytoscape.

Methods
Reader Method: uniform-node-dimensions ((fcose-layout fcose-layout))
Writer Method: (setf uniform-node-dimensions) ((fcose-layout fcose-layout))

Whether or not simple nodes (non-compound nodes) are of uniform dimensions

Source

graph-layout.lisp.

Target Slot

uniform-node-dimensions.

Generic Reader: user-const-iter (object)
Generic Writer: (setf user-const-iter) (object)
Package

cytoscape.

Methods
Reader Method: user-const-iter ((cola-layout cola-layout))
Writer Method: (setf user-const-iter) ((cola-layout cola-layout))

initial layout iterations with user-specified constraints

Source

graph-layout.lisp.

Target Slot

user-const-iter.

Generic Reader: user-panning-enabled (object)
Generic Writer: (setf user-panning-enabled) (object)
Package

cytoscape.

Methods
Reader Method: user-panning-enabled ((cytoscape-widget cytoscape-widget))
Writer Method: (setf user-panning-enabled) ((cytoscape-widget cytoscape-widget))

Whether user events (e.g. dragging the graph background) are
allowed to pan the graph. Programmatic changes to pan are unaffected by this option.

Source

cytoscape.lisp.

Target Slot

user-panning-enabled.

Generic Reader: user-zooming-enabled (object)
Generic Writer: (setf user-zooming-enabled) (object)
Package

cytoscape.

Methods
Reader Method: user-zooming-enabled ((cytoscape-widget cytoscape-widget))
Writer Method: (setf user-zooming-enabled) ((cytoscape-widget cytoscape-widget))

Whether user events (e.g. mouse wheel, pinch-to-zoom) are
allowed to zoom the graph. Programmatic changes to zoom are unaffected by this option.

Source

cytoscape.lisp.

Target Slot

user-zooming-enabled.

Generic Reader: wheel-sensitivity (object)
Generic Writer: (setf wheel-sensitivity) (object)
Package

cytoscape.

Methods
Reader Method: wheel-sensitivity ((cytoscape-widget cytoscape-widget))
Writer Method: (setf wheel-sensitivity) ((cytoscape-widget cytoscape-widget))

Changes the scroll wheel sensitivity when zooming.
This is a multiplicative modifier. So, a value between 0 and 1 reduces the sensitivity (zooms slower), and a value greater than 1 increases the sensitivity (zooms faster).

Source

cytoscape.lisp.

Target Slot

wheel-sensitivity.

Generic Reader: z-index (object)
Generic Writer: (setf z-index) (object)
Package

cytoscape.

Methods
Reader Method: z-index ((context-menu context-menu))
Writer Method: (setf z-index) ((context-menu context-menu))

the z-index of the ui div

Source

context-menu.lisp.

Target Slot

z-index.

Generic Reader: zoom (object)
Generic Writer: (setf zoom) (object)
Package

cytoscape.

Methods
Reader Method: zoom ((cytoscape-widget cytoscape-widget))
Writer Method: (setf zoom) ((cytoscape-widget cytoscape-widget))

Zoom level of the graph.

Source

cytoscape.lisp.

Target Slot

zoom.

Reader Method: zoom ((preset-layout preset-layout))
Writer Method: (setf zoom) ((preset-layout preset-layout))

The zoom level to set (prob want fit = false if set)

Source

graph-layout.lisp.

Target Slot

zoom.

Generic Reader: zooming-enabled (object)
Generic Writer: (setf zooming-enabled) (object)
Package

cytoscape.

Methods
Reader Method: zooming-enabled ((cytoscape-widget cytoscape-widget))
Writer Method: (setf zooming-enabled) ((cytoscape-widget cytoscape-widget))

Whether zooming the graph is enabled, both by user events and programmatically.

Source

cytoscape.lisp.

Target Slot

zooming-enabled.


6.1.3 Standalone methods

Method: on-custom-message ((w menu-command) content buffers)
Package

jupyter/widgets.

Source

context-menu.lisp.

Method: on-custom-message ((w graph-layout) content buffers)
Package

jupyter/widgets.

Source

graph-layout.lisp.


6.1.4 Classes

Class: breadth-first-layout

Breadth first graph layout algorithm.

Package

cytoscape.

Source

graph-layout.lisp.

Direct superclasses
Direct methods
Direct Default Initargs
InitargValue
:%model-namebreadthfirstlayoutmodel
:%view-namebreadthfirstlayoutview
Direct slots
Slot: circle

Put depths in concentric circles if true, put depths top down if false

Initargs

:circle

Readers

circle.

Writers

(setf circle).

Slot: directed

Whether the tree is directed downwards (or edges can point in any direction if false)

Initargs

:directed

Readers

directed.

Writers

(setf directed).

Slot: grid

Whether to create an even grid into which the DAG is placed (circle:false only)

Initargs

:grid

Readers

grid.

Writers

(setf grid).

Slot: maximal

Whether to shift nodes down their natural BFS depths in order to avoid upwards edges (DAGS only)

Initargs

:maximal

Readers

maximal.

Writers

(setf maximal).

Slot: roots

The roots of the trees

Initform

:null

Initargs

:roots

Readers

roots.

Writers

(setf roots).

Class: circle-layout

Circle graph layout algorithm.

Package

cytoscape.

Source

graph-layout.lisp.

Direct superclasses
Direct methods
Direct Default Initargs
InitargValue
:%model-namecirclelayoutmodel
:%view-namecirclelayoutview
Direct slots
Slot: radius

The radius of the circle

Initform

:null

Initargs

:radius

Readers

radius.

Writers

(setf radius).

Class: cola-layout

Cola graph layout algorithm.

Package

cytoscape.

Source

graph-layout.lisp.

Direct superclasses
Direct methods
Direct Default Initargs
InitargValue
:%model-namecolalayoutmodel
:%view-namecolalayoutview
Direct slots
Slot: alignment

Relative alignment constraints on nodes. Can also be set per node via data.

Initform

:null

Initargs

:alignment

Readers

alignment.

Writers

(setf alignment).

Slot: all-const-iter

Initial layout iterations with all constraints including non-overlap

Initform

:null

Initargs

:all-const-iter

Readers

all-const-iter.

Writers

(setf all-const-iter).

Slot: convergence-threshold

When the alpha value (system energy) falls below this value, the layout stops

Initform

0.01d0

Initargs

:convergence-threshold

Readers

convergence-threshold.

Writers

(setf convergence-threshold).

Slot: edge-jaccard-length

Jaccard edge length in simulation. Can also be specified per edge via data.

Initform

:null

Initargs

:edge-jaccard-length

Readers

edge-jaccard-length.

Writers

(setf edge-jaccard-length).

Slot: edge-length

Sets edge length directly in simulation. Can also be specified per edge via data.

Initform

:null

Initargs

:edge-length

Readers

edge-length.

Writers

(setf edge-length).

Slot: edge-sym-diff-length

Symmetric diff edge length in simulation. Can also be specified per edge via data.

Initform

:null

Initargs

:edge-sym-diff-length

Readers

edge-sym-diff-length.

Writers

(setf edge-sym-diff-length).

Slot: flow

use DAG/tree flow layout if specified, e.g. { axis: ’y’, minSeparation: 30 }

Initform

:null

Initargs

:flow

Readers

flow.

Writers

(setf flow).

Slot: gap-inequalities

list of inequality constraints for the gap between the nodes, e.g. [{"axis":"y", "left":node1, "right":node2, "gap":25}]

Initform

:null

Initargs

:gap-inequalities

Readers

gap-inequalities.

Writers

(setf gap-inequalities).

Slot: handle-disconnected

if true, avoids disconnected components from overlapping

Initargs

:handle-disconnected

Readers

handle-disconnected.

Writers

(setf handle-disconnected).

Slot: max-simulation-time

max length in ms to run the layout

Initform

4000

Initargs

:max-simulation-time

Readers

max-simulation-time.

Writers

(setf max-simulation-time).

Slot: unconst-iter

unconstrained initial layout iterations

Initform

:null

Initargs

:unconst-iter

Readers

unconst-iter.

Writers

(setf unconst-iter).

Slot: ungrabify-while-simulating

So you can’t drag nodes during layout

Initargs

:ungrabify-while-simulating

Readers

ungrabify-while-simulating.

Writers

(setf ungrabify-while-simulating).

Slot: user-const-iter

initial layout iterations with user-specified constraints

Initform

:null

Initargs

:user-const-iter

Readers

user-const-iter.

Writers

(setf user-const-iter).

Class: concentric-layout

Concentric graph layout algorithm.

Package

cytoscape.

Source

graph-layout.lisp.

Direct superclasses
Direct methods
Direct Default Initargs
InitargValue
:%model-nameconcentriclayoutmodel
:%view-nameconcentriclayoutview
Direct slots
Slot: equidistant

Whether levels have an equal radial distance betwen them, may cause bounding box overflow

Initargs

:equidistant

Readers

equidistant.

Writers

(setf equidistant).

Slot: min-node-spacing

Min spacing between outside of nodes (used for radius adjustment)

Initform

10

Initargs

:min-node-spacing

Readers

min-node-spacing.

Writers

(setf min-node-spacing).

Class: context-menu

Context menu for cytoscape.

Package

cytoscape.

Source

context-menu.lisp.

Direct superclasses

widget.

Direct methods
Direct Default Initargs
InitargValue
:%model-namecontextmenumodel
:%model-module+module-name+
:%model-module-version+module-version+
:%view-namecontextmenuview
:%view-module+module-name+
:%view-module-version+module-version+
Direct slots
Slot: menu-radius

the radius of the circular menu in pixels

Initform

100

Initargs

:menu-radius

Readers

menu-radius.

Writers

(setf menu-radius).

Slot: selector

Elements matching this Cytoscape.js selector will trigger this menu

Initform

"node"

Initargs

:selector

Readers

selector.

Writers

(setf selector).

Slot: commands

an array of commands to list in the menu or a function that returns the array

Initargs

:commands

Readers

commands.

Writers

(setf commands).

Slot: fill-color

the background colour of the menu

Initform

"rgba(0, 0, 0, 0.75)"

Initargs

:fill-color

Readers

fill-color.

Writers

(setf fill-color).

Slot: active-fill-color

the colour used to indicate the selected command

Initform

"rgba(1, 105, 217, 0.75)"

Initargs

:active-fill-color

Readers

active-fill-color.

Writers

(setf active-fill-color).

Slot: active-padding

additional size in pixels for the active command

Initform

20

Initargs

:active-padding

Readers

active-padding.

Writers

(setf active-padding).

Slot: indicator-size

the size in pixels of the pointer to the active command

Initform

24

Initargs

:indicator-size

Readers

indicator-size.

Writers

(setf indicator-size).

Slot: separator-width

the empty spacing in pixels between successive commands

Initform

3

Initargs

:separator-width

Readers

separator-width.

Writers

(setf separator-width).

Slot: spotlight-padding

extra spacing in pixels between the element and the spotlight

Initform

4

Initargs

:spotlight-padding

Readers

spotlight-padding.

Writers

(setf spotlight-padding).

Slot: min-spotlight-radius

the minimum radius in pixels of the spotlight

Initform

24

Initargs

:min-spotlight-radius

Readers

min-spotlight-radius.

Writers

(setf min-spotlight-radius).

Slot: max-spotlight-radius

the maximum radius in pixels of the spotlight

Initform

38

Initargs

:max-spotlight-radius

Readers

max-spotlight-radius.

Writers

(setf max-spotlight-radius).

Slot: open-menu-events

space-separated cytoscape events that will open the menu; only ‘cxttapstart‘ and/or ‘taphold‘ work here

Initform

"cxttapstart taphold"

Initargs

:open-menu-events

Readers

open-menu-events.

Writers

(setf open-menu-events).

Slot: item-color

the colour of text in the command’s content

Initform

"white"

Initargs

:item-color

Readers

item-color.

Writers

(setf item-color).

Slot: item-text-shadow-color

the text shadow colour of the command’s content

Initform

"transparent"

Initargs

:item-text-shadow-color

Readers

item-text-shadow-color.

Writers

(setf item-text-shadow-color).

Slot: z-index

the z-index of the ui div

Initform

9999

Initargs

:z-index

Readers

z-index.

Writers

(setf z-index).

Slot: at-mouse

draw menu at mouse position

Initargs

:at-mouse

Readers

at-mouse.

Writers

(setf at-mouse).

Class: cose-layout

Cose graph layout algorithm.

Package

cytoscape.

Source

graph-layout.lisp.

Direct superclasses
Direct methods
Direct Default Initargs
InitargValue
:%model-namecoselayoutmodel
:%view-namecoselayoutview
:refresh10
Direct slots
Slot: component-spacing

Extra spacing between components in non-compound graphs

Initform

40

Initargs

:component-spacing

Readers

component-spacing.

Writers

(setf component-spacing).

Slot: cooling-factor

Cooling factor (how the temperature is reduced between consecutive iterations

Initform

0.99d0

Initargs

:cooling-factor

Readers

cooling-factor.

Writers

(setf cooling-factor).

Slot: edge-elasticity

Divisor to compute edge forces. Can also be set per edge via data.

Initform

32

Initargs

:edge-elasticity

Readers

edge-elasticity.

Writers

(setf edge-elasticity).

Slot: ideal-edge-length

Ideal edge (non nested) length. Can also be set per edge via data.

Initform

32

Initargs

:ideal-edge-length

Readers

ideal-edge-length.

Writers

(setf ideal-edge-length).

Slot: initial-temp

Initial temperature (maximum node displacement)

Initform

1000.0d0

Initargs

:initial-temp

Readers

initial-temp.

Writers

(setf initial-temp).

Slot: min-temp

Lower temperature threshold (below this point the layout will end)

Initform

1.0d0

Initargs

:min-temp

Readers

min-temp.

Writers

(setf min-temp).

Slot: node-overlap

Node repulsion (overlapping) multiplier

Initform

4

Initargs

:node-overlap

Readers

node-overlap.

Writers

(setf node-overlap).

Slot: node-repulsion

Node repulsion (non overlapping) multiplier. Can also be set per node in data.

Initform

2048

Initargs

:node-repulsion

Readers

node-repulsion.

Writers

(setf node-repulsion).

Class: cytoscape-widget

Cytoscape graph widget.

Package

cytoscape.

Source

cytoscape.lisp.

Direct superclasses

dom-widget.

Direct methods
Direct Default Initargs
InitargValue
:%model-namecytoscapemodel
:%model-module+module-name+
:%model-module-version+module-version+
:%view-namecytoscapeview
:%view-module+module-name+
:%view-module-version+module-version+
Direct slots
Slot: min-zoom

A minimum bound on the zoom level of the graph. The viewport can not be scaled smaller than this zoom level.

Initform

1.0d-50

Initargs

:min-zoom

Readers

min-zoom.

Writers

(setf min-zoom).

Slot: max-zoom

A maximum bound on the zoom level of the graph. The viewport can not be scaled larger than this zoom level.

Initform

1.0d50

Initargs

:max-zoom

Readers

max-zoom.

Writers

(setf max-zoom).

Slot: zooming-enabled

Whether zooming the graph is enabled, both by user events and programmatically.

Initform

t

Initargs

:zooming-enabled

Readers

zooming-enabled.

Writers

(setf zooming-enabled).

Slot: user-zooming-enabled

Whether user events (e.g. mouse wheel, pinch-to-zoom) are
allowed to zoom the graph. Programmatic changes to zoom are unaffected by this option.

Initform

t

Initargs

:user-zooming-enabled

Readers

user-zooming-enabled.

Writers

(setf user-zooming-enabled).

Slot: panning-enabled

Whether panning the graph is enabled, both by user events sand programmatically.

Initform

t

Initargs

:panning-enabled

Readers

panning-enabled.

Writers

(setf panning-enabled).

Slot: user-panning-enabled

Whether user events (e.g. dragging the graph background) are
allowed to pan the graph. Programmatic changes to pan are unaffected by this option.

Initform

t

Initargs

:user-panning-enabled

Readers

user-panning-enabled.

Writers

(setf user-panning-enabled).

Slot: box-selection-enabled

Whether box selection (i.e. drag a box overlay around, and
release it to select) is enabled. If enabled while panning is also enabled, the user must use a modifier key (shift, alt, control, or command) to use box selection.

Initform

t

Initargs

:box-selection-enabled

Readers

box-selection-enabled.

Writers

(setf box-selection-enabled).

Slot: selection-type

A string indicating the selection behaviour from user input.
For ’additive’, a new selection made by the user adds to the set of currently selected elements. For ’single’, a new selection made by the user becomes the entire set of currently selected elements (i.e. the previous elements are unselected).

Initform

"single"

Initargs

:selection-type

Readers

selection-type.

Writers

(setf selection-type).

Slot: touch-tap-threshold

A non-negative integer that indicates the maximum allowable distance that a user may move during a tap gesture

Initform

8

Initargs

:touch-tap-threshold

Readers

touch-tap-threshold.

Writers

(setf touch-tap-threshold).

Slot: desktop-tap-threshold

A non-negative integer that indicates the maximum allowable distance that a user may move during a tap gesture

Initform

4

Initargs

:desktop-tap-threshold

Readers

desktop-tap-threshold.

Writers

(setf desktop-tap-threshold).

Slot: autolock

Whether nodes should be locked (not draggable at all) by default (if true, overrides individual node state).

Initargs

:autolock

Readers

autolock.

Writers

(setf autolock).

Slot: auto-ungrabify

Whether nodes should be ungrabified (not grabbable by user) by default (if true, overrides individual node state).

Initargs

:auto-ungrabify

Readers

auto-ungrabify.

Writers

(setf auto-ungrabify).

Slot: auto-unselectify

Whether nodes should be unselectified (immutable selection state) by default (if true, overrides individual element state).

Initargs

:auto-unselectify

Readers

auto-unselectify.

Writers

(setf auto-unselectify).

Slot: headless

A convenience option that initialises the instance to run headlessly.

Initargs

:headless

Readers

headless.

Writers

(setf headless).

Slot: style-enabled

A boolean that indicates whether styling should be used.
For headless (i.e. outside the browser) environments, display is not necessary and so neither is styling necessary — thereby speeding up your code.

Initform

t

Initargs

:style-enabled

Readers

style-enabled.

Writers

(setf style-enabled).

Slot: hide-edges-on-viewport

A rendering hint that when set to t makes the renderer
not render edges while the viewport is being manipulated. This makes panning, zooming, dragging, et cetera more responsive for large graphs.

Initargs

:hide-edges-on-viewport

Readers

hide-edges-on-viewport.

Writers

(setf hide-edges-on-viewport).

Slot: texture-on-viewport

A rendering hint that when set to true makes the
renderer use a texture during panning and zooming instead of drawing the elements, making large graphs more responsive.

Initargs

:texture-on-viewport

Readers

texture-on-viewport.

Writers

(setf texture-on-viewport).

Slot: motion-blur

A rendering hint that when set to t makes the renderer
use a motion blur effect to make the transition between frames seem smoother.

Initargs

:motion-blur

Readers

motion-blur.

Writers

(setf motion-blur).

Slot: motion-blur-opacity

When motionBlur: t, this value controls the opacity of motion blur frames.

Initform

0.2

Initargs

:motion-blur-opacity

Readers

motion-blur-opacity.

Writers

(setf motion-blur-opacity).

Slot: wheel-sensitivity

Changes the scroll wheel sensitivity when zooming.
This is a multiplicative modifier. So, a value between 0 and 1 reduces the sensitivity (zooms slower), and a value greater than 1 increases the sensitivity (zooms faster).

Initform

1.0

Initargs

:wheel-sensitivity

Readers

wheel-sensitivity.

Writers

(setf wheel-sensitivity).

Slot: graph-layouts

Layout algorithms

Initargs

:graph-layouts

Readers

graph-layouts.

Writers

(setf graph-layouts).

Slot: graph-style

The stylesheet for the graph

Initargs

:graph-style

Readers

graph-style.

Writers

(setf graph-style).

Slot: pan

Pan location of the graph.

Initform

(list (cons "x" 0) (cons "y" 0))

Initargs

:pan

Readers

pan.

Writers

(setf pan).

Slot: zoom

Zoom level of the graph.

Initform

1.0

Initargs

:zoom

Readers

zoom.

Writers

(setf zoom).

Slot: elements

The list of graph elements

Initargs

:elements

Readers

elements.

Writers

(setf elements).

Slot: context-menus

The context menus for the graph

Initargs

:context-menus

Readers

context-menus.

Writers

(setf context-menus).

Class: dagre-layout

Dagre graph layout algorithm.

Package

cytoscape.

Source

graph-layout.lisp.

Direct superclasses
Direct methods
Direct Default Initargs
InitargValue
:%model-namedagrelayoutmodel
:%view-namedagrelayoutview
Direct slots
Slot: edge-sep

the separation between adjacent edges in the same rank

Initform

:null

Initargs

:edge-sep

Readers

edge-sep.

Writers

(setf edge-sep).

Slot: edge-weight

Higher weight edges are generally made shorter and straighter than lower weight edges. Can also be set per edge via data.

Initform

1

Initargs

:edge-weight

Readers

edge-weight.

Writers

(setf edge-weight).

Slot: min-length

Number of ranks to keep between the source and target of the edge. Can also be set per edge via data.

Initform

1

Initargs

:min-length

Readers

min-length.

Writers

(setf min-length).

Slot: node-sep

the separation between adjacent nodes in the same rank

Initform

:null

Initargs

:node-sep

Readers

node-sep.

Writers

(setf node-sep).

Slot: rank-dir

’TB’ for top to bottom flow, ’LR’ for left to right,

Initform

:null

Initargs

:rank-dir

Readers

rank-dir.

Writers

(setf rank-dir).

Slot: ranker

Type of algorithm to assign a rank to each node in the input graph. Possible values: ’network-simplex’, ’tight-tree’ or ’longest-path’

Initform

:null

Initargs

:ranker

Readers

ranker.

Writers

(setf ranker).

Slot: rank-sep

the separation between each rank in the layout

Initform

:null

Initargs

:rank-sep

Readers

rank-sep.

Writers

(setf rank-sep).

Class: element

A node or an edge in a graph.

Package

cytoscape.

Source

cytoscape.lisp.

Direct superclasses

widget.

Direct methods
Direct Default Initargs
InitargValue
:%model-nameelementmodel
:%model-module+module-name+
:%model-module-version+module-version+
:%view-nameelementview
:%view-module+module-name+
:%view-module-version+module-version+
Direct slots
Slot: group

Element type. Must be either nodes or edges.

Initform

"nodes"

Initargs

:group

Readers

group.

Writers

(setf group).

Slot: removed

T if the element has been removed from the graph.

Initargs

:removed

Readers

removed.

Writers

(setf removed).

Slot: selected

Whether the element is selected in the graph.

Initargs

:selected

Readers

selected.

Writers

(setf selected).

Slot: selectable

T if the element can be selected.

Initform

t

Initargs

:selectable

Readers

selectable.

Writers

(setf selectable).

Slot: locked

T if the element will not be moved during a layout.

Initargs

:locked

Readers

locked.

Writers

(setf locked).

Slot: grabbed

T if if the element is currently grabbed.

Initargs

:grabbed

Readers

grabbed.

Writers

(setf grabbed).

Slot: grabbable

T if the element can be grabbed.

Initform

t

Initargs

:grabbable

Readers

grabbable.

Writers

(setf grabbable).

Slot: classes

A list of CSS classes

Initargs

:classes

Readers

classes.

Writers

(setf classes).

Slot: data

An alist of the properties of the element.

Initargs

:data

Readers

data.

Writers

(setf data).

Slot: position

The position of the element.

Package

common-lisp.

Initargs

:position

Readers

%position.

Writers

(setf %position).

Class: fcose-layout

fCoSE graph layout algorithm.

Package

cytoscape.

Source

graph-layout.lisp.

Direct superclasses
Direct methods
Direct Default Initargs
InitargValue
:%model-namefcose_layoutmodel
:%view-namefcose_layoutview
:nesting-factor0.1d0
:num-iter2500
:gravity0.25d0
:randomizet
Direct slots
Slot: quality

Layout quality

Initform

"default"

Initargs

:quality

Readers

quality.

Writers

(setf quality).

Slot: uniform-node-dimensions

Whether or not simple nodes (non-compound nodes) are of uniform dimensions

Initargs

:uniform-node-dimensions

Readers

uniform-node-dimensions.

Writers

(setf uniform-node-dimensions).

Slot: pack-components

Whether to pack disconnected components - valid only if randomize: true

Initform

t

Initargs

:pack-components

Readers

pack-components.

Writers

(setf pack-components).

Slot: sampling-type

False for random, true for greedy sampling

Initform

t

Initargs

:sampling-type

Readers

sampling-type.

Writers

(setf sampling-type).

Slot: sample-size

Sample size to construct distance matrix

Initform

25

Initargs

:sample-size

Readers

sample-size.

Writers

(setf sample-size).

Slot: node-separation

Separation amount between nodes

Initform

75

Initargs

:node-separation

Readers

node-separation.

Writers

(setf node-separation).

Slot: pi-tol

Power iteration tolerance

Initform

1.0e-7

Initargs

:pi-tol

Readers

pi-tol.

Writers

(setf pi-tol).

Slot: node-repulsion

Node repulsion (non overlapping) multiplier

Initform

4500

Initargs

:node-repulsion

Readers

node-repulsion.

Writers

(setf node-repulsion).

Slot: ideal-edge-length

Ideal edge (non nested) length

Initform

50

Initargs

:ideal-edge-length

Readers

ideal-edge-length.

Writers

(setf ideal-edge-length).

Slot: edge-elasticity

Divisor to compute edge forces

Initform

0.45

Initargs

:edge-elasticity

Readers

edge-elasticity.

Writers

(setf edge-elasticity).

Slot: tile

For enabling tiling

Initform

t

Initargs

:tile

Readers

tile.

Writers

(setf tile).

Slot: tile-padding-vertical

Represents the amount of the vertical space to put between the zero degree members during the tiling operation(can also be a function)

Initform

10

Initargs

:tile-padding-vertical

Readers

tile-padding-vertical.

Writers

(setf tile-padding-vertical).

Slot: tile-padding-horizontal

Represents the amount of the horizontal space to put between the zero degree members during the tiling operation(can also be a function)

Initform

10

Initargs

:tile-padding-horizontal

Readers

tile-padding-horizontal.

Writers

(setf tile-padding-horizontal).

Slot: gravity-range-compound

Gravity range (constant) for compounds

Initform

1.5d0

Initargs

:gravity-range-compound

Readers

gravity-range-compound.

Writers

(setf gravity-range-compound).

Slot: gravity-range

Gravity range (constant)

Initform

3.8d0

Initargs

:gravity-range

Readers

gravity-range.

Writers

(setf gravity-range).

Slot: gravity-compound

Gravity force (constant) for compounds

Initform

1.0d0

Initargs

:gravity-compound

Readers

gravity-compound.

Writers

(setf gravity-compound).

Slot: initial-energy-on-incremental

Initial cooling factor for incremental layout

Initform

0.3d0

Initargs

:initial-energy-on-incremental

Readers

initial-energy-on-incremental.

Writers

(setf initial-energy-on-incremental).

Class: graph-layout

Graph layout algorithm.

Package

cytoscape.

Source

graph-layout.lisp.

Direct superclasses

widget.

Direct subclasses
Direct methods
Direct Default Initargs
InitargValue
:%model-namegraphlayoutmodel
:%model-module+module-name+
:%model-module-version+module-version+
:%view-namegraphlayoutview
:%view-module+module-name+
:%view-module-version+module-version+
Direct slots
Slot: selector

Elements that the layout applies to.

Initform

"*"

Initargs

:selector

Readers

selector.

Writers

(setf selector).

Slot: on-layout-stop
Initargs

:on-layout-stop

Readers

%on-layout-stop.

Writers

(setf %on-layout-stop).

Class: grid-layout

Grid graph layout algorithm.

Package

cytoscape.

Source

graph-layout.lisp.

Direct superclasses
Direct methods
Direct Default Initargs
InitargValue
:%model-namegridlayoutmodel
:%view-namegridlayoutview
Direct slots
Slot: avoid-overlap-padding

Extra spacing around nodes when avoidOverlap: true

Initform

10

Initargs

:avoid-overlap-padding

Readers

avoid-overlap-padding.

Writers

(setf avoid-overlap-padding).

Slot: cols

Force num of cols in the grid

Initform

:null

Initargs

:cols

Readers

cols.

Writers

(setf cols).

Slot: condense

Uses all available space on false, uses minimal space on true

Initargs

:condense

Readers

condense.

Writers

(setf condense).

Slot: rows

Force num of rows in the grid

Initform

:null

Initargs

:rows

Readers

rows.

Writers

(setf rows).

Class: klay-layout

Klay graph layout algorithm.

Package

cytoscape.

Source

graph-layout.lisp.

Direct superclasses
Direct methods
Direct Default Initargs
InitargValue
:%model-nameklaylayoutmodel
:%view-nameklaylayoutview
Direct slots
Slot: add-unnecessary-bendpoints
Initargs

:add-unnecessary-bendpoints

Readers

add-unnecessary-bendpoints.

Writers

(setf add-unnecessary-bendpoints).

Slot: aspect-ratio
Initform

1.6

Initargs

:aspect-ratio

Readers

aspect-ratio.

Writers

(setf aspect-ratio).

Slot: border-spacing
Initform

20

Initargs

:border-spacing

Readers

border-spacing.

Writers

(setf border-spacing).

Slot: compact-components
Initargs

:compact-components

Readers

compact-components.

Writers

(setf compact-components).

Slot: crossing-minimization
Initform

"layer_sweep"

Initargs

:crossing-minimization

Readers

crossing-minimization.

Writers

(setf crossing-minimization).

Slot: cycle-breaking
Initform

"greedy"

Initargs

:cycle-breaking

Readers

cycle-breakingcycle-breaking.

Writers

(setf cycle-breakingcycle-breaking).

Slot: direction

UNDEFINED

Initform

20

Initargs

:direction

Readers

direction.

Writers

(setf direction).

Slot: edge-routing
Initform

"orthogonal"

Initargs

:edge-routing

Readers

edge-routing.

Writers

(setf edge-routing).

Slot: edge-spacing-factor
Initform

0.5

Initargs

:edge-spacing-factor

Readers

edge-spacing-factor.

Writers

(setf edge-spacing-factor).

Slot: feedback-edges
Initargs

:feedback-edges

Readers

feedback-edges.

Writers

(setf feedback-edges).

Slot: fixed-alignment
Initform

"none"

Initargs

:fixed-alignment

Readers

fixed-alignment.

Writers

(setf fixed-alignment).

Slot: in-layer-spacing-factor
Initform

1.0

Initargs

:in-layer-spacing-factor

Readers

in-layer-spacing-factor.

Writers

(setf in-layer-spacing-factor).

Slot: layout-hierarchy
Initargs

:layout-hierarchy

Readers

layout-hierarchy.

Writers

(setf layout-hierarchy).

Slot: linear-segments-deflection-dampening
Initform

0.3

Initargs

:linear-segments-deflection-dampening

Readers

linear-segments-deflection-dampening.

Writers

(setf linear-segments-deflection-dampening).

Slot: merge-edges
Initargs

:merge-edges

Readers

merge-edges.

Writers

(setf merge-edges).

Slot: merge-hierarchy-crossing-edges
Initform

t

Initargs

:merge-hierarchy-crossing-edges

Readers

merge-hierarchy-crossing-edges.

Writers

(setf merge-hierarchy-crossing-edges).

Slot: node-layering
Initform

"network_simplex"

Initargs

:node-layering

Readers

node-layering.

Writers

(setf node-layering).

Slot: node-placement
Initform

"brandes_koepf"

Initargs

:node-placement

Readers

node-placement.

Writers

(setf node-placement).

Slot: randomization-seed
Initform

1

Initargs

:randomization-seed

Readers

randomization-seed.

Writers

(setf randomization-seed).

Slot: route-self-loop-inside
Initargs

:route-self-loop-inside

Readers

route-self-loop-inside.

Writers

(setf route-self-loop-inside).

Slot: separate-connected-components
Initform

t

Initargs

:separate-connected-components

Readers

separate-connected-components.

Writers

(setf separate-connected-components).

Slot: spacing
Initform

20

Initargs

:spacing

Readers

spacing.

Writers

(setf spacing).

Slot: thoroughness
Initform

7

Initargs

:thoroughness

Readers

thoroughness.

Writers

(setf thoroughness).

Class: menu-command

Menu commands and selection handlers for context menus.

Package

cytoscape.

Source

context-menu.lisp.

Direct superclasses

widget.

Direct methods
Direct Default Initargs
InitargValue
:%model-namemenucommandmodel
:%model-module+module-name+
:%model-module-version+module-version+
:%view-namemenucommandview
:%view-module+module-name+
:%view-module-version+module-version+
Direct slots
Slot: fill-color

Custom background color for item.

Initargs

:fill-color

Readers

fill-color.

Writers

(setf fill-color).

Slot: content

HTML/text content to be displayed in the menu.

Initform

""

Initargs

:content

Readers

content.

Writers

(setf content).

Slot: content-style

css key:value pairs to set the command’s css in js if you want.

Initargs

:content-style

Readers

content-style.

Writers

(setf content-style).

Slot: enabled

Whether the command is selectable.

Initform

t

Initargs

:enabled

Readers

enabled.

Writers

(setf enabled).

Slot: on-select

Selection handlers

Initargs

:on-select

Readers

on-select.

Writers

(setf on-select).

Class: null-layout

Null graph layout algorithm.

Package

cytoscape.

Source

graph-layout.lisp.

Direct superclasses

graph-layout.

Direct Default Initargs
InitargValue
:%model-namenulllayoutmodel
:%view-namenulllayoutview
Class: preset-layout

Preset graph layout algorithm.

Package

cytoscape.

Source

graph-layout.lisp.

Direct superclasses
Direct methods
Direct Default Initargs
InitargValue
:%model-namepresetlayoutmodel
:%view-namepresetlayoutview
Direct slots
Slot: pan

The pan level to set (prob want fit = false if set)

Initform

:null

Initargs

:pan

Readers

pan.

Writers

(setf pan).

Slot: zoom

The zoom level to set (prob want fit = false if set)

Initform

:null

Initargs

:zoom

Readers

zoom.

Writers

(setf zoom).

Class: random-layout

Random graph layout algorithm.

Package

cytoscape.

Source

graph-layout.lisp.

Direct superclasses
Direct Default Initargs
InitargValue
:%model-namerandomlayoutmodel
:%view-namerandomlayoutview

6.2 Internals


6.2.1 Special variables

Special Variable: +module-name+
Package

cytoscape.

Source

version.lisp.

Special Variable: +module-version+
Package

cytoscape.

Source

version.lisp.


6.2.2 Generic functions

Generic Reader: %position (object)
Generic Writer: (setf %position) (object)
Package

cytoscape.

Methods
Reader Method: %position ((element element))
Writer Method: (setf %position) ((element element))

The position of the element.

Source

cytoscape.lisp.

Target Slot

position.

Generic Reader: cycle-breakingcycle-breaking (object)
Generic Writer: (setf cycle-breakingcycle-breaking) (object)
Package

cytoscape.

Methods
Reader Method: cycle-breakingcycle-breaking ((klay-layout klay-layout))
Writer Method: (setf cycle-breakingcycle-breaking) ((klay-layout klay-layout))
Source

graph-layout.lisp.

Target Slot

cycle-breaking.

Generic Reader: on-select (object)
Generic Writer: (setf on-select) (object)
Package

cytoscape.

Methods
Reader Method: on-select ((menu-command menu-command))
Writer Method: (setf on-select) ((menu-command menu-command))

Selection handlers

Source

context-menu.lisp.

Target Slot

on-select.

Generic Reader: open-menu-events (object)
Generic Writer: (setf open-menu-events) (object)
Package

cytoscape.

Methods
Reader Method: open-menu-events ((context-menu context-menu))
Writer Method: (setf open-menu-events) ((context-menu context-menu))

space-separated cytoscape events that will open the menu; only ‘cxttapstart‘ and/or ‘taphold‘ work here

Source

context-menu.lisp.

Target Slot

open-menu-events.


6.2.3 Classes

Class: animation-slots
Package

cytoscape.

Source

common-slots.lisp.

Direct subclasses
Direct methods
Direct slots
Slot: animation-duration

Duration of animation in ms, if enabled

Initform

250

Initargs

:animation-duration

Readers

animation-duration.

Writers

(setf animation-duration).

Slot: animation-easing

Easing of animation, if enabled

Initform

:null

Initargs

:animation-easing

Readers

animation-easing.

Writers

(setf animation-easing).

Class: avoid-overlap-slot
Package

cytoscape.

Source

common-slots.lisp.

Direct subclasses
Direct methods
Direct slots
Slot: avoid-overlap

Prevents node overlap, may overflow boundingBox if not enough space

Initform

t

Initargs

:avoid-overlap

Readers

avoid-overlap.

Writers

(setf avoid-overlap).

Class: bounding-box-slot
Package

cytoscape.

Source

common-slots.lisp.

Direct subclasses
Direct methods
Direct slots
Slot: bounding-box

constrain layout bounds; { x1, y1, x2, y2 } or { x1, y1, w, h }

Initform

:null

Initargs

:bounding-box

Readers

bounding-box.

Writers

(setf bounding-box).

Class: common-slots
Package

cytoscape.

Source

common-slots.lisp.

Direct subclasses
Direct methods
Direct slots
Slot: animate

Whether to animate changes to the layout

Initform

t

Initargs

:animate

Readers

animate.

Writers

(setf animate).

Slot: fit

Whether to fit the viewport to the graph

Initform

t

Initargs

:fit

Readers

fit.

Writers

(setf fit).

Slot: padding

Padding to leave between graph and viewport

Initform

30

Initargs

:padding

Readers

padding.

Writers

(setf padding).

Class: gravity-slot
Package

cytoscape.

Source

common-slots.lisp.

Direct subclasses
Direct methods
Direct slots
Slot: gravity

Gravity force (constant)

Initform

1

Initargs

:gravity

Readers

gravity.

Writers

(setf gravity).

Class: nesting-factor-slot
Package

cytoscape.

Source

common-slots.lisp.

Direct subclasses
Direct methods
Direct slots
Slot: nesting-factor

Nesting factor (multiplier) to compute ideal edge length for nested edges

Initform

1.2d0

Initargs

:nesting-factor

Readers

nesting-factor.

Writers

(setf nesting-factor).

Class: node-dimensions-include-labels-slot
Package

cytoscape.

Source

common-slots.lisp.

Direct subclasses
Direct methods
Direct slots
Slot: node-dimensions-include-labels

Includes the label when calculating node bounding boxes for the layout algorithm.

Initargs

:node-dimensions-include-labels

Readers

node-dimensions-include-labels.

Writers

(setf node-dimensions-include-labels).

Class: num-iter-slot
Package

cytoscape.

Source

common-slots.lisp.

Direct subclasses
Direct methods
Direct slots
Slot: num-iter

Maximum number of iterations to perform

Initform

1000

Initargs

:num-iter

Readers

num-iter.

Writers

(setf num-iter).

Class: radial-slots
Package

cytoscape.

Source

common-slots.lisp.

Direct subclasses
Direct methods
Direct slots
Slot: clockwise

Whether the layout should go clockwise (true) or counterclockwise/anticlockwise (false)

Initform

t

Initargs

:clockwise

Readers

clockwise.

Writers

(setf clockwise).

Slot: start-angle

Where nodes start in radians

Initform

(* 3/2 pi)

Initargs

:start-angle

Readers

start-angle.

Writers

(setf start-angle).

Slot: sweep

How many radians should be between the first and last node (defaults to full circle)

Initform

:null

Initargs

:sweep

Readers

sweep.

Writers

(setf sweep).

Class: randomize-slot
Package

cytoscape.

Source

common-slots.lisp.

Direct subclasses
Direct methods
Direct slots
Slot: randomize

Use random node positions at beginning of layout

Initargs

:randomize

Readers

randomize.

Writers

(setf randomize).

Class: refresh-slot
Package

cytoscape.

Source

common-slots.lisp.

Direct subclasses
Direct methods
Direct slots
Slot: refresh

Number of ticks per frame; higher is faster but more jerky

Initform

1

Initargs

:refresh

Readers

refresh.

Writers

(setf refresh).

Class: spacing-factor-slot
Package

cytoscape.

Source

common-slots.lisp.

Direct subclasses
Direct methods
Direct slots
Slot: spacing-factor

Applies a multiplicative factor (>0) to expand or compress the overall area that the nodes take up

Initform

:null

Initargs

:spacing-factor

Readers

spacing-factor.

Writers

(setf spacing-factor).


Appendix A Indexes


A.1 Concepts


A.2 Functions

Jump to:   %   (  
A   B   C   D   E   F   G   H   I   L   M   N   O   P   Q   R   S   T   U   W   Z  
Index Entry  Section

%
%on-layout-stop: Public generic functions
%on-layout-stop: Public generic functions
%position: Private generic functions
%position: Private generic functions

(
(setf %on-layout-stop): Public generic functions
(setf %on-layout-stop): Public generic functions
(setf %position): Private generic functions
(setf %position): Private generic functions
(setf active-fill-color): Public generic functions
(setf active-fill-color): Public generic functions
(setf active-padding): Public generic functions
(setf active-padding): Public generic functions
(setf add-unnecessary-bendpoints): Public generic functions
(setf add-unnecessary-bendpoints): Public generic functions
(setf alignment): Public generic functions
(setf alignment): Public generic functions
(setf all-const-iter): Public generic functions
(setf all-const-iter): Public generic functions
(setf animate): Public generic functions
(setf animate): Public generic functions
(setf animation-duration): Public generic functions
(setf animation-duration): Public generic functions
(setf animation-easing): Public generic functions
(setf animation-easing): Public generic functions
(setf aspect-ratio): Public generic functions
(setf aspect-ratio): Public generic functions
(setf at-mouse): Public generic functions
(setf at-mouse): Public generic functions
(setf auto-ungrabify): Public generic functions
(setf auto-ungrabify): Public generic functions
(setf auto-unselectify): Public generic functions
(setf auto-unselectify): Public generic functions
(setf autolock): Public generic functions
(setf autolock): Public generic functions
(setf avoid-overlap): Public generic functions
(setf avoid-overlap): Public generic functions
(setf avoid-overlap-padding): Public generic functions
(setf avoid-overlap-padding): Public generic functions
(setf border-spacing): Public generic functions
(setf border-spacing): Public generic functions
(setf bounding-box): Public generic functions
(setf bounding-box): Public generic functions
(setf box-selection-enabled): Public generic functions
(setf box-selection-enabled): Public generic functions
(setf circle): Public generic functions
(setf circle): Public generic functions
(setf classes): Public generic functions
(setf classes): Public generic functions
(setf clockwise): Public generic functions
(setf clockwise): Public generic functions
(setf cols): Public generic functions
(setf cols): Public generic functions
(setf commands): Public generic functions
(setf commands): Public generic functions
(setf compact-components): Public generic functions
(setf compact-components): Public generic functions
(setf component-spacing): Public generic functions
(setf component-spacing): Public generic functions
(setf condense): Public generic functions
(setf condense): Public generic functions
(setf content): Public generic functions
(setf content): Public generic functions
(setf content-style): Public generic functions
(setf content-style): Public generic functions
(setf context-menus): Public generic functions
(setf context-menus): Public generic functions
(setf convergence-threshold): Public generic functions
(setf convergence-threshold): Public generic functions
(setf cooling-factor): Public generic functions
(setf cooling-factor): Public generic functions
(setf crossing-minimization): Public generic functions
(setf crossing-minimization): Public generic functions
(setf cycle-breakingcycle-breaking): Private generic functions
(setf cycle-breakingcycle-breaking): Private generic functions
(setf data): Public generic functions
(setf data): Public generic functions
(setf desktop-tap-threshold): Public generic functions
(setf desktop-tap-threshold): Public generic functions
(setf directed): Public generic functions
(setf directed): Public generic functions
(setf direction): Public generic functions
(setf direction): Public generic functions
(setf edge-elasticity): Public generic functions
(setf edge-elasticity): Public generic functions
(setf edge-elasticity): Public generic functions
(setf edge-jaccard-length): Public generic functions
(setf edge-jaccard-length): Public generic functions
(setf edge-length): Public generic functions
(setf edge-length): Public generic functions
(setf edge-routing): Public generic functions
(setf edge-routing): Public generic functions
(setf edge-sep): Public generic functions
(setf edge-sep): Public generic functions
(setf edge-spacing-factor): Public generic functions
(setf edge-spacing-factor): Public generic functions
(setf edge-sym-diff-length): Public generic functions
(setf edge-sym-diff-length): Public generic functions
(setf edge-weight): Public generic functions
(setf edge-weight): Public generic functions
(setf elements): Public generic functions
(setf elements): Public generic functions
(setf enabled): Public generic functions
(setf enabled): Public generic functions
(setf equidistant): Public generic functions
(setf equidistant): Public generic functions
(setf feedback-edges): Public generic functions
(setf feedback-edges): Public generic functions
(setf fill-color): Public generic functions
(setf fill-color): Public generic functions
(setf fill-color): Public generic functions
(setf fit): Public generic functions
(setf fit): Public generic functions
(setf fixed-alignment): Public generic functions
(setf fixed-alignment): Public generic functions
(setf flow): Public generic functions
(setf flow): Public generic functions
(setf gap-inequalities): Public generic functions
(setf gap-inequalities): Public generic functions
(setf grabbable): Public generic functions
(setf grabbable): Public generic functions
(setf grabbed): Public generic functions
(setf grabbed): Public generic functions
(setf graph-layouts): Public generic functions
(setf graph-layouts): Public generic functions
(setf graph-style): Public generic functions
(setf graph-style): Public generic functions
(setf gravity): Public generic functions
(setf gravity): Public generic functions
(setf gravity-compound): Public generic functions
(setf gravity-compound): Public generic functions
(setf gravity-range): Public generic functions
(setf gravity-range): Public generic functions
(setf gravity-range-compound): Public generic functions
(setf gravity-range-compound): Public generic functions
(setf grid): Public generic functions
(setf grid): Public generic functions
(setf group): Public generic functions
(setf group): Public generic functions
(setf handle-disconnected): Public generic functions
(setf handle-disconnected): Public generic functions
(setf headless): Public generic functions
(setf headless): Public generic functions
(setf hide-edges-on-viewport): Public generic functions
(setf hide-edges-on-viewport): Public generic functions
(setf ideal-edge-length): Public generic functions
(setf ideal-edge-length): Public generic functions
(setf ideal-edge-length): Public generic functions
(setf in-layer-spacing-factor): Public generic functions
(setf in-layer-spacing-factor): Public generic functions
(setf indicator-size): Public generic functions
(setf indicator-size): Public generic functions
(setf initial-energy-on-incremental): Public generic functions
(setf initial-energy-on-incremental): Public generic functions
(setf initial-temp): Public generic functions
(setf initial-temp): Public generic functions
(setf item-color): Public generic functions
(setf item-color): Public generic functions
(setf item-text-shadow-color): Public generic functions
(setf item-text-shadow-color): Public generic functions
(setf layout-hierarchy): Public generic functions
(setf layout-hierarchy): Public generic functions
(setf linear-segments-deflection-dampening): Public generic functions
(setf linear-segments-deflection-dampening): Public generic functions
(setf locked): Public generic functions
(setf locked): Public generic functions
(setf max-simulation-time): Public generic functions
(setf max-simulation-time): Public generic functions
(setf max-spotlight-radius): Public generic functions
(setf max-spotlight-radius): Public generic functions
(setf max-zoom): Public generic functions
(setf max-zoom): Public generic functions
(setf maximal): Public generic functions
(setf maximal): Public generic functions
(setf menu-radius): Public generic functions
(setf menu-radius): Public generic functions
(setf merge-edges): Public generic functions
(setf merge-edges): Public generic functions
(setf merge-hierarchy-crossing-edges): Public generic functions
(setf merge-hierarchy-crossing-edges): Public generic functions
(setf min-length): Public generic functions
(setf min-length): Public generic functions
(setf min-node-spacing): Public generic functions
(setf min-node-spacing): Public generic functions
(setf min-spotlight-radius): Public generic functions
(setf min-spotlight-radius): Public generic functions
(setf min-temp): Public generic functions
(setf min-temp): Public generic functions
(setf min-zoom): Public generic functions
(setf min-zoom): Public generic functions
(setf motion-blur): Public generic functions
(setf motion-blur): Public generic functions
(setf motion-blur-opacity): Public generic functions
(setf motion-blur-opacity): Public generic functions
(setf nesting-factor): Public generic functions
(setf nesting-factor): Public generic functions
(setf node-dimensions-include-labels): Public generic functions
(setf node-dimensions-include-labels): Public generic functions
(setf node-layering): Public generic functions
(setf node-layering): Public generic functions
(setf node-overlap): Public generic functions
(setf node-overlap): Public generic functions
(setf node-placement): Public generic functions
(setf node-placement): Public generic functions
(setf node-repulsion): Public generic functions
(setf node-repulsion): Public generic functions
(setf node-repulsion): Public generic functions
(setf node-sep): Public generic functions
(setf node-sep): Public generic functions
(setf node-separation): Public generic functions
(setf node-separation): Public generic functions
(setf num-iter): Public generic functions
(setf num-iter): Public generic functions
(setf on-select): Private generic functions
(setf on-select): Private generic functions
(setf open-menu-events): Private generic functions
(setf open-menu-events): Private generic functions
(setf pack-components): Public generic functions
(setf pack-components): Public generic functions
(setf padding): Public generic functions
(setf padding): Public generic functions
(setf pan): Public generic functions
(setf pan): Public generic functions
(setf pan): Public generic functions
(setf panning-enabled): Public generic functions
(setf panning-enabled): Public generic functions
(setf pi-tol): Public generic functions
(setf pi-tol): Public generic functions
(setf quality): Public generic functions
(setf quality): Public generic functions
(setf radius): Public generic functions
(setf radius): Public generic functions
(setf randomization-seed): Public generic functions
(setf randomization-seed): Public generic functions
(setf randomize): Public generic functions
(setf randomize): Public generic functions
(setf rank-dir): Public generic functions
(setf rank-dir): Public generic functions
(setf rank-sep): Public generic functions
(setf rank-sep): Public generic functions
(setf ranker): Public generic functions
(setf ranker): Public generic functions
(setf refresh): Public generic functions
(setf refresh): Public generic functions
(setf removed): Public generic functions
(setf removed): Public generic functions
(setf roots): Public generic functions
(setf roots): Public generic functions
(setf route-self-loop-inside): Public generic functions
(setf route-self-loop-inside): Public generic functions
(setf rows): Public generic functions
(setf rows): Public generic functions
(setf sample-size): Public generic functions
(setf sample-size): Public generic functions
(setf sampling-type): Public generic functions
(setf sampling-type): Public generic functions
(setf selectable): Public generic functions
(setf selectable): Public generic functions
(setf selected): Public generic functions
(setf selected): Public generic functions
(setf selection-type): Public generic functions
(setf selection-type): Public generic functions
(setf selector): Public generic functions
(setf selector): Public generic functions
(setf selector): Public generic functions
(setf separate-connected-components): Public generic functions
(setf separate-connected-components): Public generic functions
(setf separator-width): Public generic functions
(setf separator-width): Public generic functions
(setf spacing): Public generic functions
(setf spacing): Public generic functions
(setf spacing-factor): Public generic functions
(setf spacing-factor): Public generic functions
(setf spotlight-padding): Public generic functions
(setf spotlight-padding): Public generic functions
(setf start-angle): Public generic functions
(setf start-angle): Public generic functions
(setf style-enabled): Public generic functions
(setf style-enabled): Public generic functions
(setf sweep): Public generic functions
(setf sweep): Public generic functions
(setf texture-on-viewport): Public generic functions
(setf texture-on-viewport): Public generic functions
(setf thoroughness): Public generic functions
(setf thoroughness): Public generic functions
(setf tile): Public generic functions
(setf tile): Public generic functions
(setf tile-padding-horizontal): Public generic functions
(setf tile-padding-horizontal): Public generic functions
(setf tile-padding-vertical): Public generic functions
(setf tile-padding-vertical): Public generic functions
(setf touch-tap-threshold): Public generic functions
(setf touch-tap-threshold): Public generic functions
(setf unconst-iter): Public generic functions
(setf unconst-iter): Public generic functions
(setf ungrabify-while-simulating): Public generic functions
(setf ungrabify-while-simulating): Public generic functions
(setf uniform-node-dimensions): Public generic functions
(setf uniform-node-dimensions): Public generic functions
(setf user-const-iter): Public generic functions
(setf user-const-iter): Public generic functions
(setf user-panning-enabled): Public generic functions
(setf user-panning-enabled): Public generic functions
(setf user-zooming-enabled): Public generic functions
(setf user-zooming-enabled): Public generic functions
(setf wheel-sensitivity): Public generic functions
(setf wheel-sensitivity): Public generic functions
(setf z-index): Public generic functions
(setf z-index): Public generic functions
(setf zoom): Public generic functions
(setf zoom): Public generic functions
(setf zoom): Public generic functions
(setf zooming-enabled): Public generic functions
(setf zooming-enabled): Public generic functions

A
active-fill-color: Public generic functions
active-fill-color: Public generic functions
active-padding: Public generic functions
active-padding: Public generic functions
add-graph: Public generic functions
add-graph: Public generic functions
add-graph: Public generic functions
add-unnecessary-bendpoints: Public generic functions
add-unnecessary-bendpoints: Public generic functions
alignment: Public generic functions
alignment: Public generic functions
all-const-iter: Public generic functions
all-const-iter: Public generic functions
animate: Public generic functions
animate: Public generic functions
animation-duration: Public generic functions
animation-duration: Public generic functions
animation-easing: Public generic functions
animation-easing: Public generic functions
aspect-ratio: Public generic functions
aspect-ratio: Public generic functions
at-mouse: Public generic functions
at-mouse: Public generic functions
auto-ungrabify: Public generic functions
auto-ungrabify: Public generic functions
auto-unselectify: Public generic functions
auto-unselectify: Public generic functions
autolock: Public generic functions
autolock: Public generic functions
avoid-overlap: Public generic functions
avoid-overlap: Public generic functions
avoid-overlap-padding: Public generic functions
avoid-overlap-padding: Public generic functions

B
border-spacing: Public generic functions
border-spacing: Public generic functions
bounding-box: Public generic functions
bounding-box: Public generic functions
box-selection-enabled: Public generic functions
box-selection-enabled: Public generic functions

C
center: Public ordinary functions
circle: Public generic functions
circle: Public generic functions
classes: Public generic functions
classes: Public generic functions
clockwise: Public generic functions
clockwise: Public generic functions
cols: Public generic functions
cols: Public generic functions
commands: Public generic functions
commands: Public generic functions
compact-components: Public generic functions
compact-components: Public generic functions
component-spacing: Public generic functions
component-spacing: Public generic functions
condense: Public generic functions
condense: Public generic functions
content: Public generic functions
content: Public generic functions
content-style: Public generic functions
content-style: Public generic functions
context-menus: Public generic functions
context-menus: Public generic functions
convergence-threshold: Public generic functions
convergence-threshold: Public generic functions
cooling-factor: Public generic functions
cooling-factor: Public generic functions
crossing-minimization: Public generic functions
crossing-minimization: Public generic functions
cycle-breakingcycle-breaking: Private generic functions
cycle-breakingcycle-breaking: Private generic functions

D
data: Public generic functions
data: Public generic functions
desktop-tap-threshold: Public generic functions
desktop-tap-threshold: Public generic functions
directed: Public generic functions
directed: Public generic functions
direction: Public generic functions
direction: Public generic functions

E
edge-elasticity: Public generic functions
edge-elasticity: Public generic functions
edge-elasticity: Public generic functions
edge-jaccard-length: Public generic functions
edge-jaccard-length: Public generic functions
edge-length: Public generic functions
edge-length: Public generic functions
edge-routing: Public generic functions
edge-routing: Public generic functions
edge-sep: Public generic functions
edge-sep: Public generic functions
edge-spacing-factor: Public generic functions
edge-spacing-factor: Public generic functions
edge-sym-diff-length: Public generic functions
edge-sym-diff-length: Public generic functions
edge-weight: Public generic functions
edge-weight: Public generic functions
elements: Public generic functions
elements: Public generic functions
enabled: Public generic functions
enabled: Public generic functions
equidistant: Public generic functions
equidistant: Public generic functions

F
feedback-edges: Public generic functions
feedback-edges: Public generic functions
fill-color: Public generic functions
fill-color: Public generic functions
fill-color: Public generic functions
fit: Public generic functions
fit: Public generic functions
fit-elements: Public ordinary functions
fixed-alignment: Public generic functions
fixed-alignment: Public generic functions
flow: Public generic functions
flow: Public generic functions
Function, center: Public ordinary functions
Function, fit-elements: Public ordinary functions
Function, layout: Public ordinary functions
Function, make-breadth-first-layout: Public ordinary functions
Function, make-circle-layout: Public ordinary functions
Function, make-cola-layout: Public ordinary functions
Function, make-concentric-layout: Public ordinary functions
Function, make-context-menu: Public ordinary functions
Function, make-cose-layout: Public ordinary functions
Function, make-cytoscape-widget: Public ordinary functions
Function, make-dagre-layout: Public ordinary functions
Function, make-element: Public ordinary functions
Function, make-fcose-layout: Public ordinary functions
Function, make-graph-layout: Public ordinary functions
Function, make-grid-layout: Public ordinary functions
Function, make-klay-layout: Public ordinary functions
Function, make-menu-command: Public ordinary functions
Function, make-null-layout: Public ordinary functions
Function, make-preset-layout: Public ordinary functions
Function, make-random-layout: Public ordinary functions
Function, on-layout-stop: Public ordinary functions
Function, on-menu-command-select: Public ordinary functions
Function, reset: Public ordinary functions
Function, toggle-fullscreen: Public ordinary functions

G
gap-inequalities: Public generic functions
gap-inequalities: Public generic functions
Generic Function, %on-layout-stop: Public generic functions
Generic Function, %position: Private generic functions
Generic Function, (setf %on-layout-stop): Public generic functions
Generic Function, (setf %position): Private generic functions
Generic Function, (setf active-fill-color): Public generic functions
Generic Function, (setf active-padding): Public generic functions
Generic Function, (setf add-unnecessary-bendpoints): Public generic functions
Generic Function, (setf alignment): Public generic functions
Generic Function, (setf all-const-iter): Public generic functions
Generic Function, (setf animate): Public generic functions
Generic Function, (setf animation-duration): Public generic functions
Generic Function, (setf animation-easing): Public generic functions
Generic Function, (setf aspect-ratio): Public generic functions
Generic Function, (setf at-mouse): Public generic functions
Generic Function, (setf auto-ungrabify): Public generic functions
Generic Function, (setf auto-unselectify): Public generic functions
Generic Function, (setf autolock): Public generic functions
Generic Function, (setf avoid-overlap): Public generic functions
Generic Function, (setf avoid-overlap-padding): Public generic functions
Generic Function, (setf border-spacing): Public generic functions
Generic Function, (setf bounding-box): Public generic functions
Generic Function, (setf box-selection-enabled): Public generic functions
Generic Function, (setf circle): Public generic functions
Generic Function, (setf classes): Public generic functions
Generic Function, (setf clockwise): Public generic functions
Generic Function, (setf cols): Public generic functions
Generic Function, (setf commands): Public generic functions
Generic Function, (setf compact-components): Public generic functions
Generic Function, (setf component-spacing): Public generic functions
Generic Function, (setf condense): Public generic functions
Generic Function, (setf content): Public generic functions
Generic Function, (setf content-style): Public generic functions
Generic Function, (setf context-menus): Public generic functions
Generic Function, (setf convergence-threshold): Public generic functions
Generic Function, (setf cooling-factor): Public generic functions
Generic Function, (setf crossing-minimization): Public generic functions
Generic Function, (setf cycle-breakingcycle-breaking): Private generic functions
Generic Function, (setf data): Public generic functions
Generic Function, (setf desktop-tap-threshold): Public generic functions
Generic Function, (setf directed): Public generic functions
Generic Function, (setf direction): Public generic functions
Generic Function, (setf edge-elasticity): Public generic functions
Generic Function, (setf edge-jaccard-length): Public generic functions
Generic Function, (setf edge-length): Public generic functions
Generic Function, (setf edge-routing): Public generic functions
Generic Function, (setf edge-sep): Public generic functions
Generic Function, (setf edge-spacing-factor): Public generic functions
Generic Function, (setf edge-sym-diff-length): Public generic functions
Generic Function, (setf edge-weight): Public generic functions
Generic Function, (setf elements): Public generic functions
Generic Function, (setf enabled): Public generic functions
Generic Function, (setf equidistant): Public generic functions
Generic Function, (setf feedback-edges): Public generic functions
Generic Function, (setf fill-color): Public generic functions
Generic Function, (setf fit): Public generic functions
Generic Function, (setf fixed-alignment): Public generic functions
Generic Function, (setf flow): Public generic functions
Generic Function, (setf gap-inequalities): Public generic functions
Generic Function, (setf grabbable): Public generic functions
Generic Function, (setf grabbed): Public generic functions
Generic Function, (setf graph-layouts): Public generic functions
Generic Function, (setf graph-style): Public generic functions
Generic Function, (setf gravity): Public generic functions
Generic Function, (setf gravity-compound): Public generic functions
Generic Function, (setf gravity-range): Public generic functions
Generic Function, (setf gravity-range-compound): Public generic functions
Generic Function, (setf grid): Public generic functions
Generic Function, (setf group): Public generic functions
Generic Function, (setf handle-disconnected): Public generic functions
Generic Function, (setf headless): Public generic functions
Generic Function, (setf hide-edges-on-viewport): Public generic functions
Generic Function, (setf ideal-edge-length): Public generic functions
Generic Function, (setf in-layer-spacing-factor): Public generic functions
Generic Function, (setf indicator-size): Public generic functions
Generic Function, (setf initial-energy-on-incremental): Public generic functions
Generic Function, (setf initial-temp): Public generic functions
Generic Function, (setf item-color): Public generic functions
Generic Function, (setf item-text-shadow-color): Public generic functions
Generic Function, (setf layout-hierarchy): Public generic functions
Generic Function, (setf linear-segments-deflection-dampening): Public generic functions
Generic Function, (setf locked): Public generic functions
Generic Function, (setf max-simulation-time): Public generic functions
Generic Function, (setf max-spotlight-radius): Public generic functions
Generic Function, (setf max-zoom): Public generic functions
Generic Function, (setf maximal): Public generic functions
Generic Function, (setf menu-radius): Public generic functions
Generic Function, (setf merge-edges): Public generic functions
Generic Function, (setf merge-hierarchy-crossing-edges): Public generic functions
Generic Function, (setf min-length): Public generic functions
Generic Function, (setf min-node-spacing): Public generic functions
Generic Function, (setf min-spotlight-radius): Public generic functions
Generic Function, (setf min-temp): Public generic functions
Generic Function, (setf min-zoom): Public generic functions
Generic Function, (setf motion-blur): Public generic functions
Generic Function, (setf motion-blur-opacity): Public generic functions
Generic Function, (setf nesting-factor): Public generic functions
Generic Function, (setf node-dimensions-include-labels): Public generic functions
Generic Function, (setf node-layering): Public generic functions
Generic Function, (setf node-overlap): Public generic functions
Generic Function, (setf node-placement): Public generic functions
Generic Function, (setf node-repulsion): Public generic functions
Generic Function, (setf node-sep): Public generic functions
Generic Function, (setf node-separation): Public generic functions
Generic Function, (setf num-iter): Public generic functions
Generic Function, (setf on-select): Private generic functions
Generic Function, (setf open-menu-events): Private generic functions
Generic Function, (setf pack-components): Public generic functions
Generic Function, (setf padding): Public generic functions
Generic Function, (setf pan): Public generic functions
Generic Function, (setf panning-enabled): Public generic functions
Generic Function, (setf pi-tol): Public generic functions
Generic Function, (setf quality): Public generic functions
Generic Function, (setf radius): Public generic functions
Generic Function, (setf randomization-seed): Public generic functions
Generic Function, (setf randomize): Public generic functions
Generic Function, (setf rank-dir): Public generic functions
Generic Function, (setf rank-sep): Public generic functions
Generic Function, (setf ranker): Public generic functions
Generic Function, (setf refresh): Public generic functions
Generic Function, (setf removed): Public generic functions
Generic Function, (setf roots): Public generic functions
Generic Function, (setf route-self-loop-inside): Public generic functions
Generic Function, (setf rows): Public generic functions
Generic Function, (setf sample-size): Public generic functions
Generic Function, (setf sampling-type): Public generic functions
Generic Function, (setf selectable): Public generic functions
Generic Function, (setf selected): Public generic functions
Generic Function, (setf selection-type): Public generic functions
Generic Function, (setf selector): Public generic functions
Generic Function, (setf separate-connected-components): Public generic functions
Generic Function, (setf separator-width): Public generic functions
Generic Function, (setf spacing): Public generic functions
Generic Function, (setf spacing-factor): Public generic functions
Generic Function, (setf spotlight-padding): Public generic functions
Generic Function, (setf start-angle): Public generic functions
Generic Function, (setf style-enabled): Public generic functions
Generic Function, (setf sweep): Public generic functions
Generic Function, (setf texture-on-viewport): Public generic functions
Generic Function, (setf thoroughness): Public generic functions
Generic Function, (setf tile): Public generic functions
Generic Function, (setf tile-padding-horizontal): Public generic functions
Generic Function, (setf tile-padding-vertical): Public generic functions
Generic Function, (setf touch-tap-threshold): Public generic functions
Generic Function, (setf unconst-iter): Public generic functions
Generic Function, (setf ungrabify-while-simulating): Public generic functions
Generic Function, (setf uniform-node-dimensions): Public generic functions
Generic Function, (setf user-const-iter): Public generic functions
Generic Function, (setf user-panning-enabled): Public generic functions
Generic Function, (setf user-zooming-enabled): Public generic functions
Generic Function, (setf wheel-sensitivity): Public generic functions
Generic Function, (setf z-index): Public generic functions
Generic Function, (setf zoom): Public generic functions
Generic Function, (setf zooming-enabled): Public generic functions
Generic Function, active-fill-color: Public generic functions
Generic Function, active-padding: Public generic functions
Generic Function, add-graph: Public generic functions
Generic Function, add-unnecessary-bendpoints: Public generic functions
Generic Function, alignment: Public generic functions
Generic Function, all-const-iter: Public generic functions
Generic Function, animate: Public generic functions
Generic Function, animation-duration: Public generic functions
Generic Function, animation-easing: Public generic functions
Generic Function, aspect-ratio: Public generic functions
Generic Function, at-mouse: Public generic functions
Generic Function, auto-ungrabify: Public generic functions
Generic Function, auto-unselectify: Public generic functions
Generic Function, autolock: Public generic functions
Generic Function, avoid-overlap: Public generic functions
Generic Function, avoid-overlap-padding: Public generic functions
Generic Function, border-spacing: Public generic functions
Generic Function, bounding-box: Public generic functions
Generic Function, box-selection-enabled: Public generic functions
Generic Function, circle: Public generic functions
Generic Function, classes: Public generic functions
Generic Function, clockwise: Public generic functions
Generic Function, cols: Public generic functions
Generic Function, commands: Public generic functions
Generic Function, compact-components: Public generic functions
Generic Function, component-spacing: Public generic functions
Generic Function, condense: Public generic functions
Generic Function, content: Public generic functions
Generic Function, content-style: Public generic functions
Generic Function, context-menus: Public generic functions
Generic Function, convergence-threshold: Public generic functions
Generic Function, cooling-factor: Public generic functions
Generic Function, crossing-minimization: Public generic functions
Generic Function, cycle-breakingcycle-breaking: Private generic functions
Generic Function, data: Public generic functions
Generic Function, desktop-tap-threshold: Public generic functions
Generic Function, directed: Public generic functions
Generic Function, direction: Public generic functions
Generic Function, edge-elasticity: Public generic functions
Generic Function, edge-jaccard-length: Public generic functions
Generic Function, edge-length: Public generic functions
Generic Function, edge-routing: Public generic functions
Generic Function, edge-sep: Public generic functions
Generic Function, edge-spacing-factor: Public generic functions
Generic Function, edge-sym-diff-length: Public generic functions
Generic Function, edge-weight: Public generic functions
Generic Function, elements: Public generic functions
Generic Function, enabled: Public generic functions
Generic Function, equidistant: Public generic functions
Generic Function, feedback-edges: Public generic functions
Generic Function, fill-color: Public generic functions
Generic Function, fit: Public generic functions
Generic Function, fixed-alignment: Public generic functions
Generic Function, flow: Public generic functions
Generic Function, gap-inequalities: Public generic functions
Generic Function, grabbable: Public generic functions
Generic Function, grabbed: Public generic functions
Generic Function, graph-layouts: Public generic functions
Generic Function, graph-style: Public generic functions
Generic Function, gravity: Public generic functions
Generic Function, gravity-compound: Public generic functions
Generic Function, gravity-range: Public generic functions
Generic Function, gravity-range-compound: Public generic functions
Generic Function, grid: Public generic functions
Generic Function, group: Public generic functions
Generic Function, handle-disconnected: Public generic functions
Generic Function, headless: Public generic functions
Generic Function, hide-edges-on-viewport: Public generic functions
Generic Function, ideal-edge-length: Public generic functions
Generic Function, in-layer-spacing-factor: Public generic functions
Generic Function, indicator-size: Public generic functions
Generic Function, initial-energy-on-incremental: Public generic functions
Generic Function, initial-temp: Public generic functions
Generic Function, item-color: Public generic functions
Generic Function, item-text-shadow-color: Public generic functions
Generic Function, layout-hierarchy: Public generic functions
Generic Function, linear-segments-deflection-dampening: Public generic functions
Generic Function, locked: Public generic functions
Generic Function, max-simulation-time: Public generic functions
Generic Function, max-spotlight-radius: Public generic functions
Generic Function, max-zoom: Public generic functions
Generic Function, maximal: Public generic functions
Generic Function, menu-radius: Public generic functions
Generic Function, merge-edges: Public generic functions
Generic Function, merge-hierarchy-crossing-edges: Public generic functions
Generic Function, min-length: Public generic functions
Generic Function, min-node-spacing: Public generic functions
Generic Function, min-spotlight-radius: Public generic functions
Generic Function, min-temp: Public generic functions
Generic Function, min-zoom: Public generic functions
Generic Function, motion-blur: Public generic functions
Generic Function, motion-blur-opacity: Public generic functions
Generic Function, nesting-factor: Public generic functions
Generic Function, node-dimensions-include-labels: Public generic functions
Generic Function, node-layering: Public generic functions
Generic Function, node-overlap: Public generic functions
Generic Function, node-placement: Public generic functions
Generic Function, node-repulsion: Public generic functions
Generic Function, node-sep: Public generic functions
Generic Function, node-separation: Public generic functions
Generic Function, num-iter: Public generic functions
Generic Function, on-select: Private generic functions
Generic Function, open-menu-events: Private generic functions
Generic Function, pack-components: Public generic functions
Generic Function, padding: Public generic functions
Generic Function, pan: Public generic functions
Generic Function, panning-enabled: Public generic functions
Generic Function, pi-tol: Public generic functions
Generic Function, quality: Public generic functions
Generic Function, radius: Public generic functions
Generic Function, randomization-seed: Public generic functions
Generic Function, randomize: Public generic functions
Generic Function, rank-dir: Public generic functions
Generic Function, rank-sep: Public generic functions
Generic Function, ranker: Public generic functions
Generic Function, refresh: Public generic functions
Generic Function, removed: Public generic functions
Generic Function, roots: Public generic functions
Generic Function, route-self-loop-inside: Public generic functions
Generic Function, rows: Public generic functions
Generic Function, sample-size: Public generic functions
Generic Function, sampling-type: Public generic functions
Generic Function, selectable: Public generic functions
Generic Function, selected: Public generic functions
Generic Function, selection-type: Public generic functions
Generic Function, selector: Public generic functions
Generic Function, separate-connected-components: Public generic functions
Generic Function, separator-width: Public generic functions
Generic Function, spacing: Public generic functions
Generic Function, spacing-factor: Public generic functions
Generic Function, spotlight-padding: Public generic functions
Generic Function, start-angle: Public generic functions
Generic Function, style-enabled: Public generic functions
Generic Function, sweep: Public generic functions
Generic Function, texture-on-viewport: Public generic functions
Generic Function, thoroughness: Public generic functions
Generic Function, tile: Public generic functions
Generic Function, tile-padding-horizontal: Public generic functions
Generic Function, tile-padding-vertical: Public generic functions
Generic Function, touch-tap-threshold: Public generic functions
Generic Function, unconst-iter: Public generic functions
Generic Function, ungrabify-while-simulating: Public generic functions
Generic Function, uniform-node-dimensions: Public generic functions
Generic Function, user-const-iter: Public generic functions
Generic Function, user-panning-enabled: Public generic functions
Generic Function, user-zooming-enabled: Public generic functions
Generic Function, wheel-sensitivity: Public generic functions
Generic Function, z-index: Public generic functions
Generic Function, zoom: Public generic functions
Generic Function, zooming-enabled: Public generic functions
grabbable: Public generic functions
grabbable: Public generic functions
grabbed: Public generic functions
grabbed: Public generic functions
graph-layouts: Public generic functions
graph-layouts: Public generic functions
graph-style: Public generic functions
graph-style: Public generic functions
gravity: Public generic functions
gravity: Public generic functions
gravity-compound: Public generic functions
gravity-compound: Public generic functions
gravity-range: Public generic functions
gravity-range: Public generic functions
gravity-range-compound: Public generic functions
gravity-range-compound: Public generic functions
grid: Public generic functions
grid: Public generic functions
group: Public generic functions
group: Public generic functions

H
handle-disconnected: Public generic functions
handle-disconnected: Public generic functions
headless: Public generic functions
headless: Public generic functions
hide-edges-on-viewport: Public generic functions
hide-edges-on-viewport: Public generic functions

I
ideal-edge-length: Public generic functions
ideal-edge-length: Public generic functions
ideal-edge-length: Public generic functions
in-layer-spacing-factor: Public generic functions
in-layer-spacing-factor: Public generic functions
indicator-size: Public generic functions
indicator-size: Public generic functions
initial-energy-on-incremental: Public generic functions
initial-energy-on-incremental: Public generic functions
initial-temp: Public generic functions
initial-temp: Public generic functions
item-color: Public generic functions
item-color: Public generic functions
item-text-shadow-color: Public generic functions
item-text-shadow-color: Public generic functions

L
layout: Public ordinary functions
layout-hierarchy: Public generic functions
layout-hierarchy: Public generic functions
linear-segments-deflection-dampening: Public generic functions
linear-segments-deflection-dampening: Public generic functions
locked: Public generic functions
locked: Public generic functions

M
make-breadth-first-layout: Public ordinary functions
make-circle-layout: Public ordinary functions
make-cola-layout: Public ordinary functions
make-concentric-layout: Public ordinary functions
make-context-menu: Public ordinary functions
make-cose-layout: Public ordinary functions
make-cytoscape-widget: Public ordinary functions
make-dagre-layout: Public ordinary functions
make-element: Public ordinary functions
make-fcose-layout: Public ordinary functions
make-graph-layout: Public ordinary functions
make-grid-layout: Public ordinary functions
make-klay-layout: Public ordinary functions
make-menu-command: Public ordinary functions
make-null-layout: Public ordinary functions
make-preset-layout: Public ordinary functions
make-random-layout: Public ordinary functions
max-simulation-time: Public generic functions
max-simulation-time: Public generic functions
max-spotlight-radius: Public generic functions
max-spotlight-radius: Public generic functions
max-zoom: Public generic functions
max-zoom: Public generic functions
maximal: Public generic functions
maximal: Public generic functions
menu-radius: Public generic functions
menu-radius: Public generic functions
merge-edges: Public generic functions
merge-edges: Public generic functions
merge-hierarchy-crossing-edges: Public generic functions
merge-hierarchy-crossing-edges: Public generic functions
Method, %on-layout-stop: Public generic functions
Method, %position: Private generic functions
Method, (setf %on-layout-stop): Public generic functions
Method, (setf %position): Private generic functions
Method, (setf active-fill-color): Public generic functions
Method, (setf active-padding): Public generic functions
Method, (setf add-unnecessary-bendpoints): Public generic functions
Method, (setf alignment): Public generic functions
Method, (setf all-const-iter): Public generic functions
Method, (setf animate): Public generic functions
Method, (setf animation-duration): Public generic functions
Method, (setf animation-easing): Public generic functions
Method, (setf aspect-ratio): Public generic functions
Method, (setf at-mouse): Public generic functions
Method, (setf auto-ungrabify): Public generic functions
Method, (setf auto-unselectify): Public generic functions
Method, (setf autolock): Public generic functions
Method, (setf avoid-overlap): Public generic functions
Method, (setf avoid-overlap-padding): Public generic functions
Method, (setf border-spacing): Public generic functions
Method, (setf bounding-box): Public generic functions
Method, (setf box-selection-enabled): Public generic functions
Method, (setf circle): Public generic functions
Method, (setf classes): Public generic functions
Method, (setf clockwise): Public generic functions
Method, (setf cols): Public generic functions
Method, (setf commands): Public generic functions
Method, (setf compact-components): Public generic functions
Method, (setf component-spacing): Public generic functions
Method, (setf condense): Public generic functions
Method, (setf content): Public generic functions
Method, (setf content-style): Public generic functions
Method, (setf context-menus): Public generic functions
Method, (setf convergence-threshold): Public generic functions
Method, (setf cooling-factor): Public generic functions
Method, (setf crossing-minimization): Public generic functions
Method, (setf cycle-breakingcycle-breaking): Private generic functions
Method, (setf data): Public generic functions
Method, (setf desktop-tap-threshold): Public generic functions
Method, (setf directed): Public generic functions
Method, (setf direction): Public generic functions
Method, (setf edge-elasticity): Public generic functions
Method, (setf edge-elasticity): Public generic functions
Method, (setf edge-jaccard-length): Public generic functions
Method, (setf edge-length): Public generic functions
Method, (setf edge-routing): Public generic functions
Method, (setf edge-sep): Public generic functions
Method, (setf edge-spacing-factor): Public generic functions
Method, (setf edge-sym-diff-length): Public generic functions
Method, (setf edge-weight): Public generic functions
Method, (setf elements): Public generic functions
Method, (setf enabled): Public generic functions
Method, (setf equidistant): Public generic functions
Method, (setf feedback-edges): Public generic functions
Method, (setf fill-color): Public generic functions
Method, (setf fill-color): Public generic functions
Method, (setf fit): Public generic functions
Method, (setf fixed-alignment): Public generic functions
Method, (setf flow): Public generic functions
Method, (setf gap-inequalities): Public generic functions
Method, (setf grabbable): Public generic functions
Method, (setf grabbed): Public generic functions
Method, (setf graph-layouts): Public generic functions
Method, (setf graph-style): Public generic functions
Method, (setf gravity): Public generic functions