The cytoscape-clj Reference Manual

Table of Contents

The cytoscape-clj Reference Manual

This is the cytoscape-clj Reference Manual, version 0.2.18, generated automatically by Declt version 3.0 "Montgomery Scott" on Tue Dec 22 13:14:07 2020 GMT+0.

1 Introduction

cytoscape-clj

A common-lisp-jupyter widget for cytoscape.js.

Installation

The Jupyter Lab frontend code should be installed using the following command:

jupyter-labextension install cytoscape-clj

Once the extension has been installed then widget can be loaded in a notebook using Quicklisp.

(ql:quickload :kekule-clj)

Usage

For sample notebooks please see the examples directory. The main widgets are cytoscape-widget and element. For example to create and display a graph use the following.

(make-intance 'cytoscape:cytoscape-widget
              :graph-layouts (list (make-instance 'cytoscape:cose-layout))
              :graph-style "node { label: data(id); }"
              :elements (list (make-instance 'cytoscape:element
                                             :group "nodes"
                                             :data `(("id" . "a")))
                              (make-instance 'cytoscape:element
                                             :group "nodes"
                                             :data `(("id" . "b")))
                              (make-instance 'cytoscape:element
                                             :group "nodes"
                                             :data `(("id" . "c")))
                              (make-instance 'cytoscape:element
                                             :group "edges"
                                             :data `(("source" . "a")
                                                     ("target" . "b")))
                              (make-instance 'cytoscape:element
                                             :group "edges"
                                             :data `(("source" . "a")
                                                     ("target" . "c")))
                              (make-instance 'cytoscape:element
                                             :group "edges"
                                             :data `(("source" . "b")
                                                     ("target" . "c")))))

2 Systems

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

2.1 cytoscape-clj

Author

Tarn W. Burton

License

MIT

Description

A cytoscape widget for Common Lisp Jupyter.

Version

0.2.18

Dependencies

• common-lisp-jupyter
• jsown

Source

cytoscape-clj.asd (file)

Component

src (module)

3 Modules

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

3.1 cytoscape-clj/src

Parent

cytoscape-clj (system)

Location

src/

Components

• packages.lisp (file)
• version.lisp (file)
• context-menu.lisp (file)
• graph-layout.lisp (file)
• cytoscape.lisp (file)

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.asd

Location

cytoscape-clj.asd

Systems

cytoscape-clj (system)

4.1.2 cytoscape-clj/src/packages.lisp

Parent

src (module)

Location

src/packages.lisp

Packages

cytoscape

4.1.3 cytoscape-clj/src/version.lisp

Dependency

packages.lisp (file)

Parent

src (module)

Location

src/version.lisp

Internal Definitions

• +module-name+ (special variable)
• +module-version+ (special variable)

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

Dependency

version.lisp (file)

Parent

src (module)

Location

src/context-menu.lisp

Exported Definitions

• active-fill-color (method)
• (setf active-fill-color) (method)
• active-padding (method)
• (setf active-padding) (method)
• at-mouse (method)
• (setf at-mouse) (method)
• commands (method)
• (setf commands) (method)
• content (method)
• (setf content) (method)
• content-style (method)
• (setf content-style) (method)
• context-menu (class)
• enabled (method)
• (setf enabled) (method)
• fill-color (method)
• (setf fill-color) (method)
• fill-color (method)
• (setf fill-color) (method)
• indicator-size (method)
• (setf indicator-size) (method)
• item-color (method)
• (setf item-color) (method)
• item-text-shadow-color (method)
• (setf item-text-shadow-color) (method)
• max-spotlight-radius (method)
• (setf max-spotlight-radius) (method)
• menu-command (class)
• menu-radius (method)
• (setf menu-radius) (method)
• min-spotlight-radius (method)
• (setf min-spotlight-radius) (method)
• on-menu-command-select (function)
• selector (method)
• (setf selector) (method)
• separator-width (method)
• (setf separator-width) (method)
• spotlight-padding (method)
• (setf spotlight-padding) (method)
• z-index (method)
• (setf z-index) (method)

Internal Definitions

• on-select (method)
• (setf on-select) (method)
• open-menu-events (method)
• (setf open-menu-events) (method)

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

Dependency

context-menu.lisp (file)

Parent

src (module)

Location

src/graph-layout.lisp

Exported Definitions

• %on-layout-stop (method)
• (setf %on-layout-stop) (method)
• alignment (method)
• (setf alignment) (method)
• all-const-iter (method)
• (setf all-const-iter) (method)
• animate (method)
• (setf animate) (method)
• animation-duration (method)
• (setf animation-duration) (method)
• animation-easing (method)
• (setf animation-easing) (method)
• avoid-overlap (method)
• (setf avoid-overlap) (method)
• avoid-overlap-padding (method)
• (setf avoid-overlap-padding) (method)
• bounding-box (method)
• (setf bounding-box) (method)
• breadth-first-layout (class)
• circle (method)
• (setf circle) (method)
• circle-layout (class)
• clockwise (method)
• (setf clockwise) (method)
• cola-layout (class)
• cols (method)
• (setf cols) (method)
• component-spacing (method)
• (setf component-spacing) (method)
• concentric-layout (class)
• condense (method)
• (setf condense) (method)
• convergence-threshold (method)
• (setf convergence-threshold) (method)
• cooling-factor (method)
• (setf cooling-factor) (method)
• cose-layout (class)
• dagre-layout (class)
• directed (method)
• (setf directed) (method)
• edge-elasticity (method)
• (setf edge-elasticity) (method)
• edge-elasticity (method)
• (setf edge-elasticity) (method)
• edge-jaccard-length (method)
• (setf edge-jaccard-length) (method)
• edge-length (method)
• (setf edge-length) (method)
• edge-sep (method)
• (setf edge-sep) (method)
• edge-sym-diff-length (method)
• (setf edge-sym-diff-length) (method)
• edge-weight (method)
• (setf edge-weight) (method)
• equidistant (method)
• (setf equidistant) (method)
• fcose-layout (class)
• fit (method)
• (setf fit) (method)
• flow (method)
• (setf flow) (method)
• gap-inequalities (method)
• (setf gap-inequalities) (method)
• graph-layout (class)
• gravity (method)
• (setf gravity) (method)
• gravity-compound (method)
• (setf gravity-compound) (method)
• gravity-range (method)
• (setf gravity-range) (method)
• gravity-range-compound (method)
• (setf gravity-range-compound) (method)
• grid (method)
• (setf grid) (method)
• grid-layout (class)
• handle-disconnected (method)
• (setf handle-disconnected) (method)
• ideal-edge-length (method)
• (setf ideal-edge-length) (method)
• ideal-edge-length (method)
• (setf ideal-edge-length) (method)
• initial-energy-on-incremental (method)
• (setf initial-energy-on-incremental) (method)
• initial-temp (method)
• (setf initial-temp) (method)
• max-simulation-time (method)
• (setf max-simulation-time) (method)
• maximal (method)
• (setf maximal) (method)
• min-length (method)
• (setf min-length) (method)
• min-node-spacing (method)
• (setf min-node-spacing) (method)
• min-temp (method)
• (setf min-temp) (method)
• nesting-factor (method)
• (setf nesting-factor) (method)
• node-dimensions-include-labels (method)
• (setf node-dimensions-include-labels) (method)
• node-overlap (method)
• (setf node-overlap) (method)
• node-repulsion (method)
• (setf node-repulsion) (method)
• node-repulsion (method)
• (setf node-repulsion) (method)
• node-sep (method)
• (setf node-sep) (method)
• node-separation (method)
• (setf node-separation) (method)
• null-layout (class)
• num-iter (method)
• (setf num-iter) (method)
• on-layout-stop (function)
• pack-components (method)
• (setf pack-components) (method)
• padding (method)
• (setf padding) (method)
• pan (method)
• (setf pan) (method)
• pi-tol (method)
• (setf pi-tol) (method)
• preset-layout (class)
• quality (method)
• (setf quality) (method)
• radius (method)
• (setf radius) (method)
• random-layout (class)
• randomize (method)
• (setf randomize) (method)
• rank-dir (method)
• (setf rank-dir) (method)
• rank-sep (method)
• (setf rank-sep) (method)
• ranker (method)
• (setf ranker) (method)
• refresh (method)
• (setf refresh) (method)
• roots (method)
• (setf roots) (method)
• rows (method)
• (setf rows) (method)
• sample-size (method)
• (setf sample-size) (method)
• sampling-type (method)
• (setf sampling-type) (method)
• selector (method)
• (setf selector) (method)
• spacing-factor (method)
• (setf spacing-factor) (method)
• start-angle (method)
• (setf start-angle) (method)
• sweep (method)
• (setf sweep) (method)
• tile (method)
• (setf tile) (method)
• tile-padding-horizontal (method)
• (setf tile-padding-horizontal) (method)
• tile-padding-vertical (method)
• (setf tile-padding-vertical) (method)
• unconst-iter (method)
• (setf unconst-iter) (method)
• ungrabify-while-simulating (method)
• (setf ungrabify-while-simulating) (method)
• uniform-node-dimensions (method)
• (setf uniform-node-dimensions) (method)
• user-const-iter (method)
• (setf user-const-iter) (method)
• zoom (method)
• (setf zoom) (method)

Internal Definitions

• animation-slots (class)
• avoid-overlap-slot (class)
• bounding-box-slot (class)
• common-slots (class)
• gravity-slot (class)
• nesting-factor-slot (class)
• node-dimensions-include-labels-slot (class)
• num-iter-slot (class)
• radial-slots (class)
• randomize-slot (class)
• refresh-slot (class)
• spacing-factor-slot (class)

4.1.6 cytoscape-clj/src/cytoscape.lisp

Dependency

graph-layout.lisp (file)

Parent

src (module)

Location

src/cytoscape.lisp

Exported Definitions

• add-graph (generic function)
• add-graph (method)
• auto-ungrabify (method)
• (setf auto-ungrabify) (method)
• auto-unselectify (method)
• (setf auto-unselectify) (method)
• autolock (method)
• (setf autolock) (method)
• box-selection-enabled (method)
• (setf box-selection-enabled) (method)
• center (function)
• classes (method)
• (setf classes) (method)
• context-menus (method)
• (setf context-menus) (method)
• cytoscape-widget (class)
• data (method)
• (setf data) (method)
• desktop-tap-threshold (method)
• (setf desktop-tap-threshold) (method)
• element (class)
• elements (method)
• (setf elements) (method)
• fit-elements (function)
• grabbable (method)
• (setf grabbable) (method)
• grabbed (method)
• (setf grabbed) (method)
• graph-layouts (method)
• (setf graph-layouts) (method)
• graph-style (method)
• (setf graph-style) (method)
• group (method)
• (setf group) (method)
• headless (method)
• (setf headless) (method)
• hide-edges-on-viewport (method)
• (setf hide-edges-on-viewport) (method)
• layout (function)
• locked (method)
• (setf locked) (method)
• max-zoom (method)
• (setf max-zoom) (method)
• min-zoom (method)
• (setf min-zoom) (method)
• motion-blur (method)
• (setf motion-blur) (method)
• motion-blur-opacity (method)
• (setf motion-blur-opacity) (method)
• pan (method)
• (setf pan) (method)
• panning-enabled (method)
• (setf panning-enabled) (method)
• removed (method)
• (setf removed) (method)
• reset (function)
• selectable (method)
• (setf selectable) (method)
• selected (method)
• (setf selected) (method)
• selection-type (method)
• (setf selection-type) (method)
• style-enabled (method)
• (setf style-enabled) (method)
• texture-on-viewport (method)
• (setf texture-on-viewport) (method)
• toggle-fullscreen (function)
• tooltip-source (method)
• (setf tooltip-source) (method)
• touch-tap-threshold (method)
• (setf touch-tap-threshold) (method)
• user-panning-enabled (method)
• (setf user-panning-enabled) (method)
• user-zooming-enabled (method)
• (setf user-zooming-enabled) (method)
• wheel-sensitivity (method)
• (setf wheel-sensitivity) (method)
• zoom (method)
• (setf zoom) (method)
• zooming-enabled (method)
• (setf zooming-enabled) (method)

Internal Definitions

• %position (method)
• (setf %position) (method)

5 Packages

Packages are listed by definition order.

5.1 cytoscape

Source

packages.lisp (file)

Use List

common-lisp

Exported Definitions

• %on-layout-stop (generic function)
• %on-layout-stop (method)
• (setf %on-layout-stop) (method)
• (setf %on-layout-stop) (generic function)
• active-fill-color (generic function)
• active-fill-color (method)
• (setf active-fill-color) (method)
• (setf active-fill-color) (generic function)
• active-padding (generic function)
• active-padding (method)
• (setf active-padding) (method)
• (setf active-padding) (generic function)
• add-graph (generic function)
• add-graph (method)
• alignment (generic function)
• alignment (method)
• (setf alignment) (method)
• (setf alignment) (generic function)
• all-const-iter (generic function)
• all-const-iter (method)
• (setf all-const-iter) (method)
• (setf all-const-iter) (generic function)
• animate (generic function)
• animate (method)
• (setf animate) (method)
• (setf animate) (generic function)
• animation-duration (generic function)
• animation-duration (method)
• (setf animation-duration) (method)
• (setf animation-duration) (generic function)
• animation-easing (generic function)
• animation-easing (method)
• (setf animation-easing) (method)
• (setf animation-easing) (generic function)
• at-mouse (generic function)
• at-mouse (method)
• (setf at-mouse) (method)
• (setf at-mouse) (generic function)
• auto-ungrabify (generic function)
• auto-ungrabify (method)
• (setf auto-ungrabify) (method)
• (setf auto-ungrabify) (generic function)
• auto-unselectify (generic function)
• auto-unselectify (method)
• (setf auto-unselectify) (method)
• (setf auto-unselectify) (generic function)
• autolock (generic function)
• autolock (method)
• (setf autolock) (method)
• (setf autolock) (generic function)
• avoid-overlap (generic function)
• avoid-overlap (method)
• (setf avoid-overlap) (method)
• (setf avoid-overlap) (generic function)
• avoid-overlap-padding (generic function)
• avoid-overlap-padding (method)
• (setf avoid-overlap-padding) (method)
• (setf avoid-overlap-padding) (generic function)
• bounding-box (generic function)
• bounding-box (method)
• (setf bounding-box) (method)
• (setf bounding-box) (generic function)
• box-selection-enabled (generic function)
• box-selection-enabled (method)
• (setf box-selection-enabled) (method)
• (setf box-selection-enabled) (generic function)
• breadth-first-layout (class)
• center (function)
• circle (generic function)
• circle (method)
• (setf circle) (method)
• (setf circle) (generic function)
• circle-layout (class)
• classes (generic function)
• classes (method)
• (setf classes) (method)
• (setf classes) (generic function)
• clockwise (generic function)
• clockwise (method)
• (setf clockwise) (method)
• (setf clockwise) (generic function)
• cola-layout (class)
• cols (generic function)
• cols (method)
• (setf cols) (method)
• (setf cols) (generic function)
• commands (generic function)
• commands (method)
• (setf commands) (method)
• (setf commands) (generic function)
• component-spacing (generic function)
• component-spacing (method)
• (setf component-spacing) (method)
• (setf component-spacing) (generic function)
• concentric-layout (class)
• condense (generic function)
• condense (method)
• (setf condense) (method)
• (setf condense) (generic function)
• content (generic function)
• content (method)
• (setf content) (method)
• (setf content) (generic function)
• content-style (generic function)
• content-style (method)
• (setf content-style) (method)
• (setf content-style) (generic function)
• context-menu (class)
• context-menus (generic function)
• context-menus (method)
• (setf context-menus) (method)
• (setf context-menus) (generic function)
• convergence-threshold (generic function)
• convergence-threshold (method)
• (setf convergence-threshold) (method)
• (setf convergence-threshold) (generic function)
• cooling-factor (generic function)
• cooling-factor (method)
• (setf cooling-factor) (method)
• (setf cooling-factor) (generic function)
• cose-layout (class)
• cytoscape-widget (class)
• dagre-layout (class)
• data (generic function)
• data (method)
• (setf data) (method)
• (setf data) (generic function)
• desktop-tap-threshold (generic function)
• desktop-tap-threshold (method)
• (setf desktop-tap-threshold) (method)
• (setf desktop-tap-threshold) (generic function)
• directed (generic function)
• directed (method)
• (setf directed) (method)
• (setf directed) (generic function)
• edge-elasticity (generic function)
• edge-elasticity (method)
• (setf edge-elasticity) (method)
• edge-elasticity (method)
• (setf edge-elasticity) (method)
• (setf edge-elasticity) (generic function)
• edge-jaccard-length (generic function)
• edge-jaccard-length (method)
• (setf edge-jaccard-length) (method)
• (setf edge-jaccard-length) (generic function)
• edge-length (generic function)
• edge-length (method)
• (setf edge-length) (method)
• (setf edge-length) (generic function)
• edge-sep (generic function)
• edge-sep (method)
• (setf edge-sep) (method)
• (setf edge-sep) (generic function)
• edge-sym-diff-length (generic function)
• edge-sym-diff-length (method)
• (setf edge-sym-diff-length) (method)
• (setf edge-sym-diff-length) (generic function)
• edge-weight (generic function)
• edge-weight (method)
• (setf edge-weight) (method)
• (setf edge-weight) (generic function)
• element (class)
• elements (generic function)
• elements (method)
• (setf elements) (method)
• (setf elements) (generic function)
• enabled (generic function)
• enabled (method)
• (setf enabled) (method)
• (setf enabled) (generic function)
• equidistant (generic function)
• equidistant (method)
• (setf equidistant) (method)
• (setf equidistant) (generic function)
• fcose-layout (class)
• fill-color (generic function)
• fill-color (method)
• (setf fill-color) (method)
• fill-color (method)
• (setf fill-color) (method)
• (setf fill-color) (generic function)
• fit (generic function)
• fit (method)
• (setf fit) (method)
• (setf fit) (generic function)
• fit-elements (function)
• flow (generic function)
• flow (method)
• (setf flow) (method)
• (setf flow) (generic function)
• gap-inequalities (generic function)
• gap-inequalities (method)
• (setf gap-inequalities) (method)
• (setf gap-inequalities) (generic function)
• grabbable (generic function)
• grabbable (method)
• (setf grabbable) (method)
• (setf grabbable) (generic function)
• grabbed (generic function)
• grabbed (method)
• (setf grabbed) (method)
• (setf grabbed) (generic function)
• graph-layout (class)
• graph-layouts (generic function)
• graph-layouts (method)
• (setf graph-layouts) (method)
• (setf graph-layouts) (generic function)
• graph-style (generic function)
• graph-style (method)
• (setf graph-style) (method)
• (setf graph-style) (generic function)
• gravity (generic function)
• gravity (method)
• (setf gravity) (method)
• (setf gravity) (generic function)
• gravity-compound (generic function)
• gravity-compound (method)
• (setf gravity-compound) (method)
• (setf gravity-compound) (generic function)
• gravity-range (generic function)
• gravity-range (method)
• (setf gravity-range) (method)
• (setf gravity-range) (generic function)
• gravity-range-compound (generic function)
• gravity-range-compound (method)
• (setf gravity-range-compound) (method)
• (setf gravity-range-compound) (generic function)
• grid (generic function)
• grid (method)
• (setf grid) (method)
• (setf grid) (generic function)
• grid-layout (class)
• group (generic function)
• group (method)
• (setf group) (method)
• (setf group) (generic function)
• handle-disconnected (generic function)
• handle-disconnected (method)
• (setf handle-disconnected) (method)
• (setf handle-disconnected) (generic function)
• headless (generic function)
• headless (method)
• (setf headless) (method)
• (setf headless) (generic function)
• hide-edges-on-viewport (generic function)
• hide-edges-on-viewport (method)
• (setf hide-edges-on-viewport) (method)
• (setf hide-edges-on-viewport) (generic function)
• ideal-edge-length (generic function)
• ideal-edge-length (method)
• (setf ideal-edge-length) (method)
• ideal-edge-length (method)
• (setf ideal-edge-length) (method)
• (setf ideal-edge-length) (generic function)
• indicator-size (generic function)
• indicator-size (method)
• (setf indicator-size) (method)
• (setf indicator-size) (generic function)
• initial-energy-on-incremental (generic function)
• initial-energy-on-incremental (method)
• (setf initial-energy-on-incremental) (method)
• (setf initial-energy-on-incremental) (generic function)
• initial-temp (generic function)
• initial-temp (method)
• (setf initial-temp) (method)
• (setf initial-temp) (generic function)
• item-color (generic function)
• item-color (method)
• (setf item-color) (method)
• (setf item-color) (generic function)
• item-text-shadow-color (generic function)
• item-text-shadow-color (method)
• (setf item-text-shadow-color) (method)
• (setf item-text-shadow-color) (generic function)
• layout (function)
• locked (generic function)
• locked (method)
• (setf locked) (method)
• (setf locked) (generic function)
• max-simulation-time (generic function)
• max-simulation-time (method)
• (setf max-simulation-time) (method)
• (setf max-simulation-time) (generic function)
• max-spotlight-radius (generic function)
• max-spotlight-radius (method)
• (setf max-spotlight-radius) (method)
• (setf max-spotlight-radius) (generic function)
• max-zoom (generic function)
• max-zoom (method)
• (setf max-zoom) (method)
• (setf max-zoom) (generic function)
• maximal (generic function)
• maximal (method)
• (setf maximal) (method)
• (setf maximal) (generic function)
• menu-command (class)
• menu-radius (generic function)
• menu-radius (method)
• (setf menu-radius) (method)
• (setf menu-radius) (generic function)
• min-length (generic function)
• min-length (method)
• (setf min-length) (method)
• (setf min-length) (generic function)
• min-node-spacing (generic function)
• min-node-spacing (method)
• (setf min-node-spacing) (method)
• (setf min-node-spacing) (generic function)
• min-spotlight-radius (generic function)
• min-spotlight-radius (method)
• (setf min-spotlight-radius) (method)
• (setf min-spotlight-radius) (generic function)
• min-temp (generic function)
• min-temp (method)
• (setf min-temp) (method)
• (setf min-temp) (generic function)
• min-zoom (generic function)
• min-zoom (method)
• (setf min-zoom) (method)
• (setf min-zoom) (generic function)
• motion-blur (generic function)
• motion-blur (method)
• (setf motion-blur) (method)
• (setf motion-blur) (generic function)
• motion-blur-opacity (generic function)
• motion-blur-opacity (method)
• (setf motion-blur-opacity) (method)
• (setf motion-blur-opacity) (generic function)
• nesting-factor (generic function)
• nesting-factor (method)
• (setf nesting-factor) (method)
• (setf nesting-factor) (generic function)
• node-dimensions-include-labels (generic function)
• node-dimensions-include-labels (method)
• (setf node-dimensions-include-labels) (method)
• (setf node-dimensions-include-labels) (generic function)
• node-overlap (generic function)
• node-overlap (method)
• (setf node-overlap) (method)
• (setf node-overlap) (generic function)
• node-repulsion (generic function)
• node-repulsion (method)
• (setf node-repulsion) (method)
• node-repulsion (method)
• (setf node-repulsion) (method)
• (setf node-repulsion) (generic function)
• node-sep (generic function)
• node-sep (method)
• (setf node-sep) (method)
• (setf node-sep) (generic function)
• node-separation (generic function)
• node-separation (method)
• (setf node-separation) (method)
• (setf node-separation) (generic function)
• null-layout (class)
• num-iter (generic function)
• num-iter (method)
• (setf num-iter) (method)
• (setf num-iter) (generic function)
• on-layout-stop (function)
• on-menu-command-select (function)
• pack-components (generic function)
• pack-components (method)
• (setf pack-components) (method)
• (setf pack-components) (generic function)
• padding (generic function)
• padding (method)
• (setf padding) (method)
• (setf padding) (generic function)
• pan (generic function)
• pan (method)
• (setf pan) (method)
• pan (method)
• (setf pan) (method)
• (setf pan) (generic function)
• panning-enabled (generic function)
• panning-enabled (method)
• (setf panning-enabled) (method)
• (setf panning-enabled) (generic function)
• pi-tol (generic function)
• pi-tol (method)
• (setf pi-tol) (method)
• (setf pi-tol) (generic function)
• preset-layout (class)
• quality (generic function)
• quality (method)
• (setf quality) (method)
• (setf quality) (generic function)
• radius (generic function)
• radius (method)
• (setf radius) (method)
• (setf radius) (generic function)
• random-layout (class)
• randomize (generic function)
• randomize (method)
• (setf randomize) (method)
• (setf randomize) (generic function)
• rank-dir (generic function)
• rank-dir (method)
• (setf rank-dir) (method)
• (setf rank-dir) (generic function)
• rank-sep (generic function)
• rank-sep (method)
• (setf rank-sep) (method)
• (setf rank-sep) (generic function)
• ranker (generic function)
• ranker (method)
• (setf ranker) (method)
• (setf ranker) (generic function)
• refresh (generic function)
• refresh (method)
• (setf refresh) (method)
• (setf refresh) (generic function)
• removed (generic function)
• removed (method)
• (setf removed) (method)
• (setf removed) (generic function)
• reset (function)
• roots (generic function)
• roots (method)
• (setf roots) (method)
• (setf roots) (generic function)
• rows (generic function)
• rows (method)
• (setf rows) (method)
• (setf rows) (generic function)
• sample-size (generic function)
• sample-size (method)
• (setf sample-size) (method)
• (setf sample-size) (generic function)
• sampling-type (generic function)
• sampling-type (method)
• (setf sampling-type) (method)
• (setf sampling-type) (generic function)
• selectable (generic function)
• selectable (method)
• (setf selectable) (method)
• (setf selectable) (generic function)
• selected (generic function)
• selected (method)
• (setf selected) (method)
• (setf selected) (generic function)
• selection-type (generic function)
• selection-type (method)
• (setf selection-type) (method)
• (setf selection-type) (generic function)
• selector (generic function)
• selector (method)
• (setf selector) (method)
• selector (method)
• (setf selector) (method)
• (setf selector) (generic function)
• separator-width (generic function)
• separator-width (method)
• (setf separator-width) (method)
• (setf separator-width) (generic function)
• spacing-factor (generic function)
• spacing-factor (method)
• (setf spacing-factor) (method)
• (setf spacing-factor) (generic function)
• spotlight-padding (generic function)
• spotlight-padding (method)
• (setf spotlight-padding) (method)
• (setf spotlight-padding) (generic function)
• start-angle (generic function)
• start-angle (method)
• (setf start-angle) (method)
• (setf start-angle) (generic function)
• style-enabled (generic function)
• style-enabled (method)
• (setf style-enabled) (method)
• (setf style-enabled) (generic function)
• sweep (generic function)
• sweep (method)
• (setf sweep) (method)
• (setf sweep) (generic function)
• texture-on-viewport (generic function)
• texture-on-viewport (method)
• (setf texture-on-viewport) (method)
• (setf texture-on-viewport) (generic function)
• tile (generic function)
• tile (method)
• (setf tile) (method)
• (setf tile) (generic function)
• tile-padding-horizontal (generic function)
• tile-padding-horizontal (method)
• (setf tile-padding-horizontal) (method)
• (setf tile-padding-horizontal) (generic function)
• tile-padding-vertical (generic function)
• tile-padding-vertical (method)
• (setf tile-padding-vertical) (method)
• (setf tile-padding-vertical) (generic function)
• toggle-fullscreen (function)
• tooltip-source (generic function)
• tooltip-source (method)
• (setf tooltip-source) (method)
• (setf tooltip-source) (generic function)
• touch-tap-threshold (generic function)
• touch-tap-threshold (method)
• (setf touch-tap-threshold) (method)
• (setf touch-tap-threshold) (generic function)
• unconst-iter (generic function)
• unconst-iter (method)
• (setf unconst-iter) (method)
• (setf unconst-iter) (generic function)
• ungrabify-while-simulating (generic function)
• ungrabify-while-simulating (method)
• (setf ungrabify-while-simulating) (method)
• (setf ungrabify-while-simulating) (generic function)
• uniform-node-dimensions (generic function)
• uniform-node-dimensions (method)
• (setf uniform-node-dimensions) (method)
• (setf uniform-node-dimensions) (generic function)
• user-const-iter (generic function)
• user-const-iter (method)
• (setf user-const-iter) (method)
• (setf user-const-iter) (generic function)
• user-panning-enabled (generic function)
• user-panning-enabled (method)
• (setf user-panning-enabled) (method)
• (setf user-panning-enabled) (generic function)
• user-zooming-enabled (generic function)
• user-zooming-enabled (method)
• (setf user-zooming-enabled) (method)
• (setf user-zooming-enabled) (generic function)
• wheel-sensitivity (generic function)
• wheel-sensitivity (method)
• (setf wheel-sensitivity) (method)
• (setf wheel-sensitivity) (generic function)
• z-index (generic function)
• z-index (method)
• (setf z-index) (method)
• (setf z-index) (generic function)
• zoom (generic function)
• zoom (method)
• (setf zoom) (method)
• zoom (method)
• (setf zoom) (method)
• (setf zoom) (generic function)
• zooming-enabled (generic function)
• zooming-enabled (method)
• (setf zooming-enabled) (method)
• (setf zooming-enabled) (generic function)

Internal Definitions

• %position (generic function)
• %position (method)
• (setf %position) (method)
• (setf %position) (generic function)
• +module-name+ (special variable)
• +module-version+ (special variable)
• animation-slots (class)
• avoid-overlap-slot (class)
• bounding-box-slot (class)
• common-slots (class)
• gravity-slot (class)
• nesting-factor-slot (class)
• node-dimensions-include-labels-slot (class)
• num-iter-slot (class)
• on-select (generic function)
• on-select (method)
• (setf on-select) (method)
• (setf on-select) (generic function)
• open-menu-events (generic function)
• open-menu-events (method)
• (setf open-menu-events) (method)
• (setf open-menu-events) (generic function)
• radial-slots (class)
• randomize-slot (class)
• refresh-slot (class)
• spacing-factor-slot (class)

6 Definitions

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

6.1 Exported definitions

6.1.1 Functions

Function: center INSTANCE

Package

cytoscape

Source

cytoscape.lisp (file)

Function: fit-elements INSTANCE &key ELEMENTS PADDING

Package

cytoscape

Source

cytoscape.lisp (file)

Function: layout INSTANCE

Package

cytoscape

Source

cytoscape.lisp (file)

Function: on-layout-stop WIDGET HANDLER

Package

cytoscape

Source

graph-layout.lisp (file)

Function: on-menu-command-select WIDGET HANDLER

Add a new selection handler for a menu command.

Package

cytoscape

Source

context-menu.lisp (file)

Function: reset INSTANCE

Package

cytoscape

Source

cytoscape.lisp (file)

Function: toggle-fullscreen INSTANCE

Package

cytoscape

Source

cytoscape.lisp (file)

6.1.2 Generic functions

Generic Function: %on-layout-stop OBJECT

Generic Function: (setf %on-layout-stop) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: %on-layout-stop (GRAPH-LAYOUT graph-layout)

automatically generated reader method

Source

graph-layout.lisp (file)

Method: (setf %on-layout-stop) NEW-VALUE (GRAPH-LAYOUT graph-layout)

automatically generated writer method

Source

graph-layout.lisp (file)

Generic Function: active-fill-color OBJECT

Generic Function: (setf active-fill-color) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: active-fill-color (CONTEXT-MENU context-menu)

Method: (setf active-fill-color) NEW-VALUE (CONTEXT-MENU context-menu)

the colour used to indicate the selected command

Source

context-menu.lisp (file)

Generic Function: active-padding OBJECT

Generic Function: (setf active-padding) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: active-padding (CONTEXT-MENU context-menu)

Method: (setf active-padding) NEW-VALUE (CONTEXT-MENU context-menu)

additional size in pixels for the active command

Source

context-menu.lisp (file)

Generic Function: add-graph INSTANCE VALUE &rest ARGS

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

Package

cytoscape

Source

cytoscape.lisp (file)

Methods

Method: add-graph INSTANCE (VALUE list) &rest ARGS

Generic Function: alignment OBJECT

Generic Function: (setf alignment) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: alignment (COLA-LAYOUT cola-layout)

Method: (setf alignment) NEW-VALUE (COLA-LAYOUT cola-layout)

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

Source

graph-layout.lisp (file)

Generic Function: all-const-iter OBJECT

Generic Function: (setf all-const-iter) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: all-const-iter (COLA-LAYOUT cola-layout)

Method: (setf all-const-iter) NEW-VALUE (COLA-LAYOUT cola-layout)

Initial layout iterations with all constraints including non-overlap

Source

graph-layout.lisp (file)

Generic Function: animate OBJECT

Generic Function: (setf animate) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: animate (COMMON-SLOTS common-slots)

Method: (setf animate) NEW-VALUE (COMMON-SLOTS common-slots)

Whether to animate changes to the layout

Source

graph-layout.lisp (file)

Generic Function: animation-duration OBJECT

Generic Function: (setf animation-duration) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: animation-duration (ANIMATION-SLOTS animation-slots)

Method: (setf animation-duration) NEW-VALUE (ANIMATION-SLOTS animation-slots)

Duration of animation in ms, if enabled

Source

graph-layout.lisp (file)

Generic Function: animation-easing OBJECT

Generic Function: (setf animation-easing) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: animation-easing (ANIMATION-SLOTS animation-slots)

Method: (setf animation-easing) NEW-VALUE (ANIMATION-SLOTS animation-slots)

Easing of animation, if enabled

Source

graph-layout.lisp (file)

Generic Function: at-mouse OBJECT

Generic Function: (setf at-mouse) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: at-mouse (CONTEXT-MENU context-menu)

Method: (setf at-mouse) NEW-VALUE (CONTEXT-MENU context-menu)

draw menu at mouse position

Source

context-menu.lisp (file)

Generic Function: auto-ungrabify OBJECT

Generic Function: (setf auto-ungrabify) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: auto-ungrabify (CYTOSCAPE-WIDGET cytoscape-widget)

Method: (setf auto-ungrabify) NEW-VALUE (CYTOSCAPE-WIDGET cytoscape-widget)

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

Source

cytoscape.lisp (file)

Generic Function: auto-unselectify OBJECT

Generic Function: (setf auto-unselectify) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: auto-unselectify (CYTOSCAPE-WIDGET cytoscape-widget)

Method: (setf auto-unselectify) NEW-VALUE (CYTOSCAPE-WIDGET cytoscape-widget)

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

Source

cytoscape.lisp (file)

Generic Function: autolock OBJECT

Generic Function: (setf autolock) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: autolock (CYTOSCAPE-WIDGET cytoscape-widget)

Method: (setf autolock) NEW-VALUE (CYTOSCAPE-WIDGET cytoscape-widget)

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

Source

cytoscape.lisp (file)

Generic Function: avoid-overlap OBJECT

Generic Function: (setf avoid-overlap) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: avoid-overlap (AVOID-OVERLAP-SLOT avoid-overlap-slot)

Method: (setf avoid-overlap) NEW-VALUE (AVOID-OVERLAP-SLOT avoid-overlap-slot)

Prevents node overlap, may overflow boundingBox if not enough space

Source

graph-layout.lisp (file)

Generic Function: avoid-overlap-padding OBJECT

Generic Function: (setf avoid-overlap-padding) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: avoid-overlap-padding (GRID-LAYOUT grid-layout)

Method: (setf avoid-overlap-padding) NEW-VALUE (GRID-LAYOUT grid-layout)

Extra spacing around nodes when avoidOverlap: true

Source

graph-layout.lisp (file)

Generic Function: bounding-box OBJECT

Generic Function: (setf bounding-box) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: bounding-box (BOUNDING-BOX-SLOT bounding-box-slot)

Method: (setf bounding-box) NEW-VALUE (BOUNDING-BOX-SLOT bounding-box-slot)

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

Source

graph-layout.lisp (file)

Generic Function: box-selection-enabled OBJECT

Generic Function: (setf box-selection-enabled) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: box-selection-enabled (CYTOSCAPE-WIDGET cytoscape-widget)

Method: (setf box-selection-enabled) NEW-VALUE (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 (file)

Generic Function: circle OBJECT

Generic Function: (setf circle) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: circle (BREADTH-FIRST-LAYOUT breadth-first-layout)

Method: (setf circle) NEW-VALUE (BREADTH-FIRST-LAYOUT breadth-first-layout)

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

Source

graph-layout.lisp (file)

Generic Function: classes OBJECT

Generic Function: (setf classes) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: classes (ELEMENT element)

Method: (setf classes) NEW-VALUE (ELEMENT element)

A list of CSS classes

Source

cytoscape.lisp (file)

Generic Function: clockwise OBJECT

Generic Function: (setf clockwise) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: clockwise (RADIAL-SLOTS radial-slots)

Method: (setf clockwise) NEW-VALUE (RADIAL-SLOTS radial-slots)

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

Source

graph-layout.lisp (file)

Generic Function: cols OBJECT

Generic Function: (setf cols) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: cols (GRID-LAYOUT grid-layout)

Method: (setf cols) NEW-VALUE (GRID-LAYOUT grid-layout)

Force num of cols in the grid

Source

graph-layout.lisp (file)

Generic Function: commands OBJECT

Generic Function: (setf commands) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: commands (CONTEXT-MENU context-menu)

Method: (setf commands) NEW-VALUE (CONTEXT-MENU context-menu)

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

Source

context-menu.lisp (file)

Generic Function: component-spacing OBJECT

Generic Function: (setf component-spacing) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: component-spacing (COSE-LAYOUT cose-layout)

Method: (setf component-spacing) NEW-VALUE (COSE-LAYOUT cose-layout)

Extra spacing between components in non-compound graphs

Source

graph-layout.lisp (file)

Generic Function: condense OBJECT

Generic Function: (setf condense) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: condense (GRID-LAYOUT grid-layout)

Method: (setf condense) NEW-VALUE (GRID-LAYOUT grid-layout)

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

Source

graph-layout.lisp (file)

Generic Function: content OBJECT

Generic Function: (setf content) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: content (MENU-COMMAND menu-command)

Method: (setf content) NEW-VALUE (MENU-COMMAND menu-command)

HTML/text content to be displayed in the menu.

Source

context-menu.lisp (file)

Generic Function: content-style OBJECT

Generic Function: (setf content-style) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: content-style (MENU-COMMAND menu-command)

Method: (setf content-style) NEW-VALUE (MENU-COMMAND menu-command)

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

Source

context-menu.lisp (file)

Generic Function: context-menus OBJECT

Generic Function: (setf context-menus) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: context-menus (CYTOSCAPE-WIDGET cytoscape-widget)

Method: (setf context-menus) NEW-VALUE (CYTOSCAPE-WIDGET cytoscape-widget)

The context menus for the graph

Source

cytoscape.lisp (file)

Generic Function: convergence-threshold OBJECT

Generic Function: (setf convergence-threshold) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: convergence-threshold (COLA-LAYOUT cola-layout)

Method: (setf convergence-threshold) NEW-VALUE (COLA-LAYOUT cola-layout)

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

Source

graph-layout.lisp (file)

Generic Function: cooling-factor OBJECT

Generic Function: (setf cooling-factor) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: cooling-factor (COSE-LAYOUT cose-layout)

Method: (setf cooling-factor) NEW-VALUE (COSE-LAYOUT cose-layout)

Cooling factor (how the temperature is reduced between consecutive iterations

Source

graph-layout.lisp (file)

Generic Function: data OBJECT

Generic Function: (setf data) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: data (ELEMENT element)

Method: (setf data) NEW-VALUE (ELEMENT element)

An alist of the properties of the element.

Source

cytoscape.lisp (file)

Generic Function: desktop-tap-threshold OBJECT

Generic Function: (setf desktop-tap-threshold) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: desktop-tap-threshold (CYTOSCAPE-WIDGET cytoscape-widget)

Method: (setf desktop-tap-threshold) NEW-VALUE (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 (file)

Generic Function: directed OBJECT

Generic Function: (setf directed) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: directed (BREADTH-FIRST-LAYOUT breadth-first-layout)

Method: (setf directed) NEW-VALUE (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 (file)

Generic Function: edge-elasticity OBJECT

Generic Function: (setf edge-elasticity) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: edge-elasticity (FCOSE-LAYOUT fcose-layout)

Method: (setf edge-elasticity) NEW-VALUE (FCOSE-LAYOUT fcose-layout)

Divisor to compute edge forces

Source

graph-layout.lisp (file)

Method: edge-elasticity (COSE-LAYOUT cose-layout)

Method: (setf edge-elasticity) NEW-VALUE (COSE-LAYOUT cose-layout)

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

Source

graph-layout.lisp (file)

Generic Function: edge-jaccard-length OBJECT

Generic Function: (setf edge-jaccard-length) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: edge-jaccard-length (COLA-LAYOUT cola-layout)

Method: (setf edge-jaccard-length) NEW-VALUE (COLA-LAYOUT cola-layout)

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

Source

graph-layout.lisp (file)

Generic Function: edge-length OBJECT

Generic Function: (setf edge-length) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: edge-length (COLA-LAYOUT cola-layout)

Method: (setf edge-length) NEW-VALUE (COLA-LAYOUT cola-layout)

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

Source

graph-layout.lisp (file)

Generic Function: edge-sep OBJECT

Generic Function: (setf edge-sep) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: edge-sep (DAGRE-LAYOUT dagre-layout)

Method: (setf edge-sep) NEW-VALUE (DAGRE-LAYOUT dagre-layout)

the separation between adjacent edges in the same rank

Source

graph-layout.lisp (file)

Generic Function: edge-sym-diff-length OBJECT

Generic Function: (setf edge-sym-diff-length) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: edge-sym-diff-length (COLA-LAYOUT cola-layout)

Method: (setf edge-sym-diff-length) NEW-VALUE (COLA-LAYOUT cola-layout)

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

Source

graph-layout.lisp (file)

Generic Function: edge-weight OBJECT

Generic Function: (setf edge-weight) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: edge-weight (DAGRE-LAYOUT dagre-layout)

Method: (setf edge-weight) NEW-VALUE (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 (file)

Generic Function: elements OBJECT

Generic Function: (setf elements) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: elements (CYTOSCAPE-WIDGET cytoscape-widget)

Method: (setf elements) NEW-VALUE (CYTOSCAPE-WIDGET cytoscape-widget)

The list of graph elements

Source

cytoscape.lisp (file)

Generic Function: enabled OBJECT

Generic Function: (setf enabled) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: enabled (MENU-COMMAND menu-command)

Method: (setf enabled) NEW-VALUE (MENU-COMMAND menu-command)

Whether the command is selectable.

Source

context-menu.lisp (file)

Generic Function: equidistant OBJECT

Generic Function: (setf equidistant) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: equidistant (CONCENTRIC-LAYOUT concentric-layout)

Method: (setf equidistant) NEW-VALUE (CONCENTRIC-LAYOUT concentric-layout)

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

Source

graph-layout.lisp (file)

Generic Function: fill-color OBJECT

Generic Function: (setf fill-color) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: fill-color (CONTEXT-MENU context-menu)

Method: (setf fill-color) NEW-VALUE (CONTEXT-MENU context-menu)

the background colour of the menu

Source

context-menu.lisp (file)

Method: fill-color (MENU-COMMAND menu-command)

Method: (setf fill-color) NEW-VALUE (MENU-COMMAND menu-command)

Custom background color for item.

Source

context-menu.lisp (file)

Generic Function: fit OBJECT

Generic Function: (setf fit) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: fit (COMMON-SLOTS common-slots)

Method: (setf fit) NEW-VALUE (COMMON-SLOTS common-slots)

Whether to fit the viewport to the graph

Source

graph-layout.lisp (file)

Generic Function: flow OBJECT

Generic Function: (setf flow) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: flow (COLA-LAYOUT cola-layout)

Method: (setf flow) NEW-VALUE (COLA-LAYOUT cola-layout)

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

Source

graph-layout.lisp (file)

Generic Function: gap-inequalities OBJECT

Generic Function: (setf gap-inequalities) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: gap-inequalities (COLA-LAYOUT cola-layout)

Method: (setf gap-inequalities) NEW-VALUE (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 (file)

Generic Function: grabbable OBJECT

Generic Function: (setf grabbable) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: grabbable (ELEMENT element)

Method: (setf grabbable) NEW-VALUE (ELEMENT element)

T if the element can be grabbed.

Source

cytoscape.lisp (file)

Generic Function: grabbed OBJECT

Generic Function: (setf grabbed) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: grabbed (ELEMENT element)

Method: (setf grabbed) NEW-VALUE (ELEMENT element)

T if if the element is currently grabbed.

Source

cytoscape.lisp (file)

Generic Function: graph-layouts OBJECT

Generic Function: (setf graph-layouts) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: graph-layouts (CYTOSCAPE-WIDGET cytoscape-widget)

Method: (setf graph-layouts) NEW-VALUE (CYTOSCAPE-WIDGET cytoscape-widget)

Layout algorithms

Source

cytoscape.lisp (file)

Generic Function: graph-style OBJECT

Generic Function: (setf graph-style) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: graph-style (CYTOSCAPE-WIDGET cytoscape-widget)

Method: (setf graph-style) NEW-VALUE (CYTOSCAPE-WIDGET cytoscape-widget)

The stylesheet for the graph

Source

cytoscape.lisp (file)

Generic Function: gravity OBJECT

Generic Function: (setf gravity) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: gravity (GRAVITY-SLOT gravity-slot)

Method: (setf gravity) NEW-VALUE (GRAVITY-SLOT gravity-slot)

Gravity force (constant)

Source

graph-layout.lisp (file)

Generic Function: gravity-compound OBJECT

Generic Function: (setf gravity-compound) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: gravity-compound (FCOSE-LAYOUT fcose-layout)

Method: (setf gravity-compound) NEW-VALUE (FCOSE-LAYOUT fcose-layout)

Gravity force (constant) for compounds

Source

graph-layout.lisp (file)

Generic Function: gravity-range OBJECT

Generic Function: (setf gravity-range) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: gravity-range (FCOSE-LAYOUT fcose-layout)

Method: (setf gravity-range) NEW-VALUE (FCOSE-LAYOUT fcose-layout)

Gravity range (constant)

Source

graph-layout.lisp (file)

Generic Function: gravity-range-compound OBJECT

Generic Function: (setf gravity-range-compound) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: gravity-range-compound (FCOSE-LAYOUT fcose-layout)

Method: (setf gravity-range-compound) NEW-VALUE (FCOSE-LAYOUT fcose-layout)

Gravity range (constant) for compounds

Source

graph-layout.lisp (file)

Generic Function: grid OBJECT

Generic Function: (setf grid) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: grid (BREADTH-FIRST-LAYOUT breadth-first-layout)

Method: (setf grid) NEW-VALUE (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 (file)

Generic Function: group OBJECT

Generic Function: (setf group) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: group (ELEMENT element)

Method: (setf group) NEW-VALUE (ELEMENT element)

Element type. Must be either nodes or edges.

Source

cytoscape.lisp (file)

Generic Function: handle-disconnected OBJECT

Generic Function: (setf handle-disconnected) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: handle-disconnected (COLA-LAYOUT cola-layout)

Method: (setf handle-disconnected) NEW-VALUE (COLA-LAYOUT cola-layout)

if true, avoids disconnected components from overlapping

Source

graph-layout.lisp (file)

Generic Function: headless OBJECT

Generic Function: (setf headless) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: headless (CYTOSCAPE-WIDGET cytoscape-widget)

Method: (setf headless) NEW-VALUE (CYTOSCAPE-WIDGET cytoscape-widget)

A convenience option that initialises the instance to run headlessly.

Source

cytoscape.lisp (file)

Generic Function: hide-edges-on-viewport OBJECT

Generic Function: (setf hide-edges-on-viewport) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: hide-edges-on-viewport (CYTOSCAPE-WIDGET cytoscape-widget)

Method: (setf hide-edges-on-viewport) NEW-VALUE (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 (file)

Generic Function: ideal-edge-length OBJECT

Generic Function: (setf ideal-edge-length) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: ideal-edge-length (FCOSE-LAYOUT fcose-layout)

Method: (setf ideal-edge-length) NEW-VALUE (FCOSE-LAYOUT fcose-layout)

Ideal edge (non nested) length

Source

graph-layout.lisp (file)

Method: ideal-edge-length (COSE-LAYOUT cose-layout)

Method: (setf ideal-edge-length) NEW-VALUE (COSE-LAYOUT cose-layout)

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

Source

graph-layout.lisp (file)

Generic Function: indicator-size OBJECT

Generic Function: (setf indicator-size) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: indicator-size (CONTEXT-MENU context-menu)

Method: (setf indicator-size) NEW-VALUE (CONTEXT-MENU context-menu)

the size in pixels of the pointer to the active command

Source

context-menu.lisp (file)

Generic Function: initial-energy-on-incremental OBJECT

Generic Function: (setf initial-energy-on-incremental) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: initial-energy-on-incremental (FCOSE-LAYOUT fcose-layout)

Method: (setf initial-energy-on-incremental) NEW-VALUE (FCOSE-LAYOUT fcose-layout)

Initial cooling factor for incremental layout

Source

graph-layout.lisp (file)

Generic Function: initial-temp OBJECT

Generic Function: (setf initial-temp) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: initial-temp (COSE-LAYOUT cose-layout)

Method: (setf initial-temp) NEW-VALUE (COSE-LAYOUT cose-layout)

Initial temperature (maximum node displacement)

Source

graph-layout.lisp (file)

Generic Function: item-color OBJECT

Generic Function: (setf item-color) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: item-color (CONTEXT-MENU context-menu)

Method: (setf item-color) NEW-VALUE (CONTEXT-MENU context-menu)

the colour of text in the command’s content

Source

context-menu.lisp (file)

Generic Function: item-text-shadow-color OBJECT

Generic Function: (setf item-text-shadow-color) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: item-text-shadow-color (CONTEXT-MENU context-menu)

Method: (setf item-text-shadow-color) NEW-VALUE (CONTEXT-MENU context-menu)

the text shadow colour of the command’s content

Source

context-menu.lisp (file)

Generic Function: locked OBJECT

Generic Function: (setf locked) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: locked (ELEMENT element)

Method: (setf locked) NEW-VALUE (ELEMENT element)

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

Source

cytoscape.lisp (file)

Generic Function: max-simulation-time OBJECT

Generic Function: (setf max-simulation-time) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: max-simulation-time (COLA-LAYOUT cola-layout)

Method: (setf max-simulation-time) NEW-VALUE (COLA-LAYOUT cola-layout)

max length in ms to run the layout

Source

graph-layout.lisp (file)

Generic Function: max-spotlight-radius OBJECT

Generic Function: (setf max-spotlight-radius) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: max-spotlight-radius (CONTEXT-MENU context-menu)

Method: (setf max-spotlight-radius) NEW-VALUE (CONTEXT-MENU context-menu)

the maximum radius in pixels of the spotlight

Source

context-menu.lisp (file)

Generic Function: max-zoom OBJECT

Generic Function: (setf max-zoom) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: max-zoom (CYTOSCAPE-WIDGET cytoscape-widget)

Method: (setf max-zoom) NEW-VALUE (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 (file)

Generic Function: maximal OBJECT

Generic Function: (setf maximal) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: maximal (BREADTH-FIRST-LAYOUT breadth-first-layout)

Method: (setf maximal) NEW-VALUE (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 (file)

Generic Function: menu-radius OBJECT

Generic Function: (setf menu-radius) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: menu-radius (CONTEXT-MENU context-menu)

Method: (setf menu-radius) NEW-VALUE (CONTEXT-MENU context-menu)

the radius of the circular menu in pixels

Source

context-menu.lisp (file)

Generic Function: min-length OBJECT

Generic Function: (setf min-length) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: min-length (DAGRE-LAYOUT dagre-layout)

Method: (setf min-length) NEW-VALUE (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 (file)

Generic Function: min-node-spacing OBJECT

Generic Function: (setf min-node-spacing) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: min-node-spacing (CONCENTRIC-LAYOUT concentric-layout)

Method: (setf min-node-spacing) NEW-VALUE (CONCENTRIC-LAYOUT concentric-layout)

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

Source

graph-layout.lisp (file)

Generic Function: min-spotlight-radius OBJECT

Generic Function: (setf min-spotlight-radius) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: min-spotlight-radius (CONTEXT-MENU context-menu)

Method: (setf min-spotlight-radius) NEW-VALUE (CONTEXT-MENU context-menu)

the minimum radius in pixels of the spotlight

Source

context-menu.lisp (file)

Generic Function: min-temp OBJECT

Generic Function: (setf min-temp) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: min-temp (COSE-LAYOUT cose-layout)

Method: (setf min-temp) NEW-VALUE (COSE-LAYOUT cose-layout)

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

Source

graph-layout.lisp (file)

Generic Function: min-zoom OBJECT

Generic Function: (setf min-zoom) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: min-zoom (CYTOSCAPE-WIDGET cytoscape-widget)

Method: (setf min-zoom) NEW-VALUE (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 (file)

Generic Function: motion-blur OBJECT

Generic Function: (setf motion-blur) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: motion-blur (CYTOSCAPE-WIDGET cytoscape-widget)

Method: (setf motion-blur) NEW-VALUE (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 (file)

Generic Function: motion-blur-opacity OBJECT

Generic Function: (setf motion-blur-opacity) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: motion-blur-opacity (CYTOSCAPE-WIDGET cytoscape-widget)

Method: (setf motion-blur-opacity) NEW-VALUE (CYTOSCAPE-WIDGET cytoscape-widget)

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

Source

cytoscape.lisp (file)

Generic Function: nesting-factor OBJECT

Generic Function: (setf nesting-factor) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: nesting-factor (NESTING-FACTOR-SLOT nesting-factor-slot)

Method: (setf nesting-factor) NEW-VALUE (NESTING-FACTOR-SLOT nesting-factor-slot)

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

Source

graph-layout.lisp (file)

Generic Function: node-dimensions-include-labels OBJECT

Generic Function: (setf node-dimensions-include-labels) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: node-dimensions-include-labels (NODE-DIMENSIONS-INCLUDE-LABELS-SLOT node-dimensions-include-labels-slot)

Method: (setf node-dimensions-include-labels) NEW-VALUE (NODE-DIMENSIONS-INCLUDE-LABELS-SLOT node-dimensions-include-labels-slot)

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

Source

graph-layout.lisp (file)

Generic Function: node-overlap OBJECT

Generic Function: (setf node-overlap) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: node-overlap (COSE-LAYOUT cose-layout)

Method: (setf node-overlap) NEW-VALUE (COSE-LAYOUT cose-layout)

Node repulsion (overlapping) multiplier

Source

graph-layout.lisp (file)

Generic Function: node-repulsion OBJECT

Generic Function: (setf node-repulsion) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: node-repulsion (FCOSE-LAYOUT fcose-layout)

Method: (setf node-repulsion) NEW-VALUE (FCOSE-LAYOUT fcose-layout)

Node repulsion (non overlapping) multiplier

Source

graph-layout.lisp (file)

Method: node-repulsion (COSE-LAYOUT cose-layout)

Method: (setf node-repulsion) NEW-VALUE (COSE-LAYOUT cose-layout)

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

Source

graph-layout.lisp (file)

Generic Function: node-sep OBJECT

Generic Function: (setf node-sep) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: node-sep (DAGRE-LAYOUT dagre-layout)

Method: (setf node-sep) NEW-VALUE (DAGRE-LAYOUT dagre-layout)

the separation between adjacent nodes in the same rank

Source

graph-layout.lisp (file)

Generic Function: node-separation OBJECT

Generic Function: (setf node-separation) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: node-separation (FCOSE-LAYOUT fcose-layout)

Method: (setf node-separation) NEW-VALUE (FCOSE-LAYOUT fcose-layout)

Separation amount between nodes

Source

graph-layout.lisp (file)

Generic Function: num-iter OBJECT

Generic Function: (setf num-iter) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: num-iter (NUM-ITER-SLOT num-iter-slot)

Method: (setf num-iter) NEW-VALUE (NUM-ITER-SLOT num-iter-slot)

Maximum number of iterations to perform

Source

graph-layout.lisp (file)

Generic Function: pack-components OBJECT

Generic Function: (setf pack-components) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: pack-components (FCOSE-LAYOUT fcose-layout)

Method: (setf pack-components) NEW-VALUE (FCOSE-LAYOUT fcose-layout)

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

Source

graph-layout.lisp (file)

Generic Function: padding OBJECT

Generic Function: (setf padding) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: padding (COMMON-SLOTS common-slots)

Method: (setf padding) NEW-VALUE (COMMON-SLOTS common-slots)

Padding to leave between graph and viewport

Source

graph-layout.lisp (file)

Generic Function: pan OBJECT

Generic Function: (setf pan) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: pan (CYTOSCAPE-WIDGET cytoscape-widget)

Method: (setf pan) NEW-VALUE (CYTOSCAPE-WIDGET cytoscape-widget)

Pan location of the graph.

Source

cytoscape.lisp (file)

Method: pan (PRESET-LAYOUT preset-layout)

Method: (setf pan) NEW-VALUE (PRESET-LAYOUT preset-layout)

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

Source

graph-layout.lisp (file)

Generic Function: panning-enabled OBJECT

Generic Function: (setf panning-enabled) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: panning-enabled (CYTOSCAPE-WIDGET cytoscape-widget)

Method: (setf panning-enabled) NEW-VALUE (CYTOSCAPE-WIDGET cytoscape-widget)

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

Source

cytoscape.lisp (file)

Generic Function: pi-tol OBJECT

Generic Function: (setf pi-tol) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: pi-tol (FCOSE-LAYOUT fcose-layout)

Method: (setf pi-tol) NEW-VALUE (FCOSE-LAYOUT fcose-layout)

Power iteration tolerance

Source

graph-layout.lisp (file)

Generic Function: quality OBJECT

Generic Function: (setf quality) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: quality (FCOSE-LAYOUT fcose-layout)

Method: (setf quality) NEW-VALUE (FCOSE-LAYOUT fcose-layout)

Layout quality

Source

graph-layout.lisp (file)

Generic Function: radius OBJECT

Generic Function: (setf radius) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: radius (CIRCLE-LAYOUT circle-layout)

Method: (setf radius) NEW-VALUE (CIRCLE-LAYOUT circle-layout)

The radius of the circle

Source

graph-layout.lisp (file)

Generic Function: randomize OBJECT

Generic Function: (setf randomize) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: randomize (RANDOMIZE-SLOT randomize-slot)

Method: (setf randomize) NEW-VALUE (RANDOMIZE-SLOT randomize-slot)

Use random node positions at beginning of layout

Source

graph-layout.lisp (file)

Generic Function: rank-dir OBJECT

Generic Function: (setf rank-dir) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: rank-dir (DAGRE-LAYOUT dagre-layout)

Method: (setf rank-dir) NEW-VALUE (DAGRE-LAYOUT dagre-layout)

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

Source

graph-layout.lisp (file)

Generic Function: rank-sep OBJECT

Generic Function: (setf rank-sep) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: rank-sep (DAGRE-LAYOUT dagre-layout)

Method: (setf rank-sep) NEW-VALUE (DAGRE-LAYOUT dagre-layout)

the separation between each rank in the layout

Source

graph-layout.lisp (file)

Generic Function: ranker OBJECT

Generic Function: (setf ranker) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: ranker (DAGRE-LAYOUT dagre-layout)

Method: (setf ranker) NEW-VALUE (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 (file)

Generic Function: refresh OBJECT

Generic Function: (setf refresh) NEW-VALUE OBJECT

Package

cytoscape

Methods

Method: refresh (REFRESH-SLOT refresh-slot)

Method: (setf refresh) NEW-VALUE (REFRESH-SLOT refresh-slot)

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

Source

graph-layout.lisp (file)