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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.
• Introduction | What cytoscape-clj is all about | |
• Systems | The systems documentation | |
• Modules | The modules documentation | |
• Files | The files documentation | |
• Packages | The packages documentation | |
• Definitions | The symbols documentation | |
• Indexes | Concepts, functions, variables and data types |
A common-lisp-jupyter widget for cytoscape.js.
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)
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")))))
Next: Modules, Previous: Introduction, Up: Top [Contents][Index]
The main system appears first, followed by any subsystem dependency.
• The cytoscape-clj system |
Tarn W. Burton
MIT
A cytoscape widget for Common Lisp Jupyter.
0.2.18
cytoscape-clj.asd (file)
src (module)
Modules are listed depth-first from the system components tree.
• The cytoscape-clj/src module |
cytoscape-clj (system)
src/
Files are sorted by type and then listed depth-first from the systems components trees.
• Lisp files |
Next: The cytoscape-clj/src/packages․lisp file, Previous: Lisp files, Up: Lisp files [Contents][Index]
cytoscape-clj.asd
cytoscape-clj (system)
Next: The cytoscape-clj/src/version․lisp file, Previous: The cytoscape-clj․asd file, Up: Lisp files [Contents][Index]
Next: The cytoscape-clj/src/context-menu․lisp file, Previous: The cytoscape-clj/src/packages․lisp file, Up: Lisp files [Contents][Index]
packages.lisp (file)
src (module)
src/version.lisp
Next: The cytoscape-clj/src/graph-layout․lisp file, Previous: The cytoscape-clj/src/version․lisp file, Up: Lisp files [Contents][Index]
version.lisp (file)
src (module)
src/context-menu.lisp
Next: The cytoscape-clj/src/cytoscape․lisp file, Previous: The cytoscape-clj/src/context-menu․lisp file, Up: Lisp files [Contents][Index]
context-menu.lisp (file)
src (module)
src/graph-layout.lisp
Previous: The cytoscape-clj/src/graph-layout․lisp file, Up: Lisp files [Contents][Index]
graph-layout.lisp (file)
src (module)
src/cytoscape.lisp
Next: Definitions, Previous: Files, Up: Top [Contents][Index]
Packages are listed by definition order.
• The cytoscape package |
packages.lisp (file)
common-lisp
Definitions are sorted by export status, category, package, and then by lexicographic order.
• Exported definitions | ||
• Internal definitions |
Next: Internal definitions, Previous: Definitions, Up: Definitions [Contents][Index]
• Exported functions | ||
• Exported generic functions | ||
• Exported classes |
Next: Exported generic functions, Previous: Exported definitions, Up: Exported definitions [Contents][Index]
cytoscape.lisp (file)
cytoscape.lisp (file)
cytoscape.lisp (file)
graph-layout.lisp (file)
Add a new selection handler for a menu command.
context-menu.lisp (file)
cytoscape.lisp (file)
cytoscape.lisp (file)
Next: Exported classes, Previous: Exported functions, Up: Exported definitions [Contents][Index]
automatically generated reader method
graph-layout.lisp (file)
automatically generated writer method
graph-layout.lisp (file)
the colour used to indicate the selected command
context-menu.lisp (file)
additional size in pixels for the active command
context-menu.lisp (file)
Add a graph to a cytoscape widget based on value type.
cytoscape.lisp (file)
Relative alignment constraints on nodes. Can also be set per node via data.
graph-layout.lisp (file)
Initial layout iterations with all constraints including non-overlap
graph-layout.lisp (file)
Whether to animate changes to the layout
graph-layout.lisp (file)
Duration of animation in ms, if enabled
graph-layout.lisp (file)
Easing of animation, if enabled
graph-layout.lisp (file)
draw menu at mouse position
context-menu.lisp (file)
Whether nodes should be ungrabified (not grabbable by user) by default (if true, overrides individual node state).
cytoscape.lisp (file)
Whether nodes should be unselectified (immutable selection state) by default (if true, overrides individual element state).
cytoscape.lisp (file)
Whether nodes should be locked (not draggable at all) by default (if true, overrides individual node state).
cytoscape.lisp (file)
Prevents node overlap, may overflow boundingBox if not enough space
graph-layout.lisp (file)
Extra spacing around nodes when avoidOverlap: true
graph-layout.lisp (file)
constrain layout bounds; { x1, y1, x2, y2 } or { x1, y1, w, h }
graph-layout.lisp (file)
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.
cytoscape.lisp (file)
Put depths in concentric circles if true, put depths top down if false
graph-layout.lisp (file)
A list of CSS classes
cytoscape.lisp (file)
Whether the layout should go clockwise (true) or counterclockwise/anticlockwise (false)
graph-layout.lisp (file)
Force num of cols in the grid
graph-layout.lisp (file)
an array of commands to list in the menu or a function that returns the array
context-menu.lisp (file)
Extra spacing between components in non-compound graphs
graph-layout.lisp (file)
Uses all available space on false, uses minimal space on true
graph-layout.lisp (file)
HTML/text content to be displayed in the menu.
context-menu.lisp (file)
css key:value pairs to set the command’s css in js if you want.
context-menu.lisp (file)
The context menus for the graph
cytoscape.lisp (file)
When the alpha value (system energy) falls below this value, the layout stops
graph-layout.lisp (file)
Cooling factor (how the temperature is reduced between consecutive iterations
graph-layout.lisp (file)
An alist of the properties of the element.
cytoscape.lisp (file)
A non-negative integer that indicates the maximum allowable distance that a user may move during a tap gesture
cytoscape.lisp (file)
Whether the tree is directed downwards (or edges can point in any direction if false)
graph-layout.lisp (file)
Divisor to compute edge forces
graph-layout.lisp (file)
Divisor to compute edge forces. Can also be set per edge via data.
graph-layout.lisp (file)
Jaccard edge length in simulation. Can also be specified per edge via data.
graph-layout.lisp (file)
Sets edge length directly in simulation. Can also be specified per edge via data.
graph-layout.lisp (file)
the separation between adjacent edges in the same rank
graph-layout.lisp (file)
Symmetric diff edge length in simulation. Can also be specified per edge via data.
graph-layout.lisp (file)
Higher weight edges are generally made shorter and straighter than lower weight edges. Can also be set per edge via data.
graph-layout.lisp (file)
The list of graph elements
cytoscape.lisp (file)
Whether the command is selectable.
context-menu.lisp (file)
Whether levels have an equal radial distance betwen them, may cause bounding box overflow
graph-layout.lisp (file)
the background colour of the menu
context-menu.lisp (file)
Custom background color for item.
context-menu.lisp (file)
Whether to fit the viewport to the graph
graph-layout.lisp (file)
use DAG/tree flow layout if specified, e.g. { axis: ’y’, minSeparation: 30 }
graph-layout.lisp (file)
list of inequality constraints for the gap between the nodes, e.g. [{"axis":"y", "left":node1, "right":node2, "gap":25}]
graph-layout.lisp (file)
T if the element can be grabbed.
cytoscape.lisp (file)
T if if the element is currently grabbed.
cytoscape.lisp (file)
Layout algorithms
cytoscape.lisp (file)
The stylesheet for the graph
cytoscape.lisp (file)
Gravity force (constant)
graph-layout.lisp (file)
Gravity force (constant) for compounds
graph-layout.lisp (file)
Gravity range (constant)
graph-layout.lisp (file)
Gravity range (constant) for compounds
graph-layout.lisp (file)
Whether to create an even grid into which the DAG is placed (circle:false only)
graph-layout.lisp (file)
Element type. Must be either nodes or edges.
cytoscape.lisp (file)
if true, avoids disconnected components from overlapping
graph-layout.lisp (file)
A convenience option that initialises the instance to run headlessly.
cytoscape.lisp (file)
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.
cytoscape.lisp (file)
Ideal edge (non nested) length
graph-layout.lisp (file)
Ideal edge (non nested) length. Can also be set per edge via data.
graph-layout.lisp (file)
the size in pixels of the pointer to the active command
context-menu.lisp (file)
Initial cooling factor for incremental layout
graph-layout.lisp (file)
Initial temperature (maximum node displacement)
graph-layout.lisp (file)
the colour of text in the command’s content
context-menu.lisp (file)
the text shadow colour of the command’s content
context-menu.lisp (file)
T if the element will not be moved during a layout.
cytoscape.lisp (file)
max length in ms to run the layout
graph-layout.lisp (file)
the maximum radius in pixels of the spotlight
context-menu.lisp (file)
A maximum bound on the zoom level of the graph. The viewport can not be scaled larger than this zoom level.
cytoscape.lisp (file)
Whether to shift nodes down their natural BFS depths in order to avoid upwards edges (DAGS only)
graph-layout.lisp (file)
the radius of the circular menu in pixels
context-menu.lisp (file)
Number of ranks to keep between the source and target of the edge. Can also be set per edge via data.
graph-layout.lisp (file)
Min spacing between outside of nodes (used for radius adjustment)
graph-layout.lisp (file)
the minimum radius in pixels of the spotlight
context-menu.lisp (file)
Lower temperature threshold (below this point the layout will end)
graph-layout.lisp (file)
A minimum bound on the zoom level of the graph. The viewport can not be scaled smaller than this zoom level.
cytoscape.lisp (file)
A rendering hint that when set to t makes the renderer
use a motion blur effect to make the transition between frames seem smoother.
cytoscape.lisp (file)
When motionBlur: t, this value controls the opacity of motion blur frames.
cytoscape.lisp (file)
Nesting factor (multiplier) to compute ideal edge length for nested edges
graph-layout.lisp (file)
Includes the label when calculating node bounding boxes for the layout algorithm.
graph-layout.lisp (file)
Node repulsion (overlapping) multiplier
graph-layout.lisp (file)
Node repulsion (non overlapping) multiplier
graph-layout.lisp (file)
Node repulsion (non overlapping) multiplier. Can also be set per node in data.
graph-layout.lisp (file)
the separation between adjacent nodes in the same rank
graph-layout.lisp (file)
Separation amount between nodes
graph-layout.lisp (file)
Maximum number of iterations to perform
graph-layout.lisp (file)
Whether to pack disconnected components - valid only if randomize: true
graph-layout.lisp (file)
Padding to leave between graph and viewport
graph-layout.lisp (file)
Pan location of the graph.
cytoscape.lisp (file)
The pan level to set (prob want fit = false if set)
graph-layout.lisp (file)
Whether panning the graph is enabled, both by user events sand programmatically.
cytoscape.lisp (file)
Power iteration tolerance
graph-layout.lisp (file)
Layout quality
graph-layout.lisp (file)
The radius of the circle
graph-layout.lisp (file)
Use random node positions at beginning of layout
graph-layout.lisp (file)
’TB’ for top to bottom flow, ’LR’ for left to right,
graph-layout.lisp (file)
the separation between each rank in the layout
graph-layout.lisp (file)
Type of algorithm to assign a rank to each node in the input graph. Possible values: ’network-simplex’, ’tight-tree’ or ’longest-path’
graph-layout.lisp (file)
Number of ticks per frame; higher is faster but more jerky
graph-layout.lisp (file)
T if the element has been removed from the graph.
cytoscape.lisp (file)
The roots of the trees
graph-layout.lisp (file)
Force num of rows in the grid
graph-layout.lisp (file)
Sample size to construct distance matrix
graph-layout.lisp (file)
False for random, true for greedy sampling
graph-layout.lisp (file)
T if the element can be selected.
cytoscape.lisp (file)
Whether the element is selected in the graph.
cytoscape.lisp (file)
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).
cytoscape.lisp (file)
Elements that the layout applies to.
graph-layout.lisp (file)
Elements matching this Cytoscape.js selector will trigger this menu
context-menu.lisp (file)
the empty spacing in pixels between successive commands
context-menu.lisp (file)
Applies a multiplicative factor (>0) to expand or compress the overall area that the nodes take up
graph-layout.lisp (file)
extra spacing in pixels between the element and the spotlight
context-menu.lisp (file)
Where nodes start in radians
graph-layout.lisp (file)
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.
cytoscape.lisp (file)
How many radians should be between the first and last node (defaults to full circle)
graph-layout.lisp (file)
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.
cytoscape.lisp (file)
For enabling tiling
graph-layout.lisp (file)
Represents the amount of the horizontal space to put between the zero degree members during the tiling operation(can also be a function)
graph-layout.lisp (file)
Represents the amount of the vertical space to put between the zero degree members during the tiling operation(can also be a function)
graph-layout.lisp (file)
Field name in data of the tooltips.
cytoscape.lisp (file)
A non-negative integer that indicates the maximum allowable distance that a user may move during a tap gesture
cytoscape.lisp (file)
unconstrained initial layout iterations
graph-layout.lisp (file)
So you can’t drag nodes during layout
graph-layout.lisp (file)
Whether or not simple nodes (non-compound nodes) are of uniform dimensions
graph-layout.lisp (file)
initial layout iterations with user-specified constraints
graph-layout.lisp (file)
Whether user events (e.g. dragging the graph background) are
allowed to pan the graph. Programmatic changes to pan are unaffected by
this option.
cytoscape.lisp (file)
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.
cytoscape.lisp (file)
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).
cytoscape.lisp (file)
the z-index of the ui div
context-menu.lisp (file)
Zoom level of the graph.
cytoscape.lisp (file)
The zoom level to set (prob want fit = false if set)
graph-layout.lisp (file)
Whether zooming the graph is enabled, both by user events and programmatically.
cytoscape.lisp (file)
Previous: Exported generic functions, Up: Exported definitions [Contents][Index]
Breadth first graph layout algorithm.
graph-layout.lisp (file)
Put depths in concentric circles if true, put depths top down if false
:circle
circle (generic function)
(setf circle) (generic function)
Whether the tree is directed downwards (or edges can point in any direction if false)
:directed
directed (generic function)
(setf directed) (generic function)
Whether to create an even grid into which the DAG is placed (circle:false only)
:grid
grid (generic function)
(setf grid) (generic function)
Whether to shift nodes down their natural BFS depths in order to avoid upwards edges (DAGS only)
:maximal
maximal (generic function)
(setf maximal) (generic function)
The roots of the trees
:roots
:null
roots (generic function)
(setf roots) (generic function)
Initarg | Value |
---|---|
:%model-name | "breadthfirstlayoutmodel" |
:%view-name | "breadthfirstlayoutview" |
Circle graph layout algorithm.
graph-layout.lisp (file)
The radius of the circle
:radius
:null
radius (generic function)
(setf radius) (generic function)
Initarg | Value |
---|---|
:%model-name | "circlelayoutmodel" |
:%view-name | "circlelayoutview" |
Cola graph layout algorithm.
graph-layout.lisp (file)
Relative alignment constraints on nodes. Can also be set per node via data.
:alignment
:null
alignment (generic function)
(setf alignment) (generic function)
Initial layout iterations with all constraints including non-overlap
:all-const-iter
:null
all-const-iter (generic function)
(setf all-const-iter) (generic function)
When the alpha value (system energy) falls below this value, the layout stops
:convergence-threshold
0.01d0
convergence-threshold (generic function)
(setf convergence-threshold) (generic function)
Jaccard edge length in simulation. Can also be specified per edge via data.
:edge-jaccard-length
:null
edge-jaccard-length (generic function)
(setf edge-jaccard-length) (generic function)
Sets edge length directly in simulation. Can also be specified per edge via data.
:edge-length
:null
edge-length (generic function)
(setf edge-length) (generic function)
Symmetric diff edge length in simulation. Can also be specified per edge via data.
:edge-sym-diff-length
:null
edge-sym-diff-length (generic function)
(setf edge-sym-diff-length) (generic function)
use DAG/tree flow layout if specified, e.g. { axis: ’y’, minSeparation: 30 }
:flow
:null
flow (generic function)
(setf flow) (generic function)
list of inequality constraints for the gap between the nodes, e.g. [{"axis":"y", "left":node1, "right":node2, "gap":25}]
:gap-inequalities
:null
gap-inequalities (generic function)
(setf gap-inequalities) (generic function)
if true, avoids disconnected components from overlapping
:handle-disconnected
handle-disconnected (generic function)
(setf handle-disconnected) (generic function)
max length in ms to run the layout
:max-simulation-time
4000
max-simulation-time (generic function)
(setf max-simulation-time) (generic function)
unconstrained initial layout iterations
:unconst-iter
:null
unconst-iter (generic function)
(setf unconst-iter) (generic function)
So you can’t drag nodes during layout
:ungrabify-while-simulating
ungrabify-while-simulating (generic function)
(setf ungrabify-while-simulating) (generic function)
initial layout iterations with user-specified constraints
:user-const-iter
:null
user-const-iter (generic function)
(setf user-const-iter) (generic function)
Initarg | Value |
---|---|
:%model-name | "colalayoutmodel" |
:%view-name | "colalayoutview" |
Concentric graph layout algorithm.
graph-layout.lisp (file)
Whether levels have an equal radial distance betwen them, may cause bounding box overflow
:equidistant
equidistant (generic function)
(setf equidistant) (generic function)
Min spacing between outside of nodes (used for radius adjustment)
:min-node-spacing
10
min-node-spacing (generic function)
(setf min-node-spacing) (generic function)
Initarg | Value |
---|---|
:%model-name | "concentriclayoutmodel" |
:%view-name | "concentriclayoutview" |
Context menu for cytoscape.
context-menu.lisp (file)
widget (class)
the radius of the circular menu in pixels
:menu-radius
100
menu-radius (generic function)
(setf menu-radius) (generic function)
Elements matching this Cytoscape.js selector will trigger this menu
:selector
"node"
selector (generic function)
(setf selector) (generic function)
an array of commands to list in the menu or a function that returns the array
:commands
commands (generic function)
(setf commands) (generic function)
the background colour of the menu
:fill-color
"rgba(0, 0, 0, 0.75)"
fill-color (generic function)
(setf fill-color) (generic function)
the colour used to indicate the selected command
:active-fill-color
"rgba(1, 105, 217, 0.75)"
active-fill-color (generic function)
(setf active-fill-color) (generic function)
additional size in pixels for the active command
:active-padding
20
active-padding (generic function)
(setf active-padding) (generic function)
the size in pixels of the pointer to the active command
:indicator-size
24
indicator-size (generic function)
(setf indicator-size) (generic function)
the empty spacing in pixels between successive commands
:separator-width
3
separator-width (generic function)
(setf separator-width) (generic function)
extra spacing in pixels between the element and the spotlight
:spotlight-padding
4
spotlight-padding (generic function)
(setf spotlight-padding) (generic function)
the minimum radius in pixels of the spotlight
:min-spotlight-radius
24
min-spotlight-radius (generic function)
(setf min-spotlight-radius) (generic function)
the maximum radius in pixels of the spotlight
:max-spotlight-radius
38
max-spotlight-radius (generic function)
(setf max-spotlight-radius) (generic function)
space-separated cytoscape events that will open the menu; only ‘cxttapstart‘ and/or ‘taphold‘ work here
:open-menu-events
"cxttapstart taphold"
open-menu-events (generic function)
(setf open-menu-events) (generic function)
the colour of text in the command’s content
:item-color
"white"
item-color (generic function)
(setf item-color) (generic function)
the text shadow colour of the command’s content
:item-text-shadow-color
"transparent"
item-text-shadow-color (generic function)
(setf item-text-shadow-color) (generic function)
the z-index of the ui div
:z-index
9999
z-index (generic function)
(setf z-index) (generic function)
draw menu at mouse position
:at-mouse
at-mouse (generic function)
(setf at-mouse) (generic function)
Initarg | Value |
---|---|
:%model-name | "contextmenumodel" |
:%model-module | cytoscape::+module-name+ |
:%model-module-version | cytoscape::+module-version+ |
:%view-name | "contextmenuview" |
:%view-module | cytoscape::+module-name+ |
:%view-module-version | cytoscape::+module-version+ |
Cose graph layout algorithm.
graph-layout.lisp (file)
Extra spacing between components in non-compound graphs
:component-spacing
40
component-spacing (generic function)
(setf component-spacing) (generic function)
Cooling factor (how the temperature is reduced between consecutive iterations
:cooling-factor
0.99d0
cooling-factor (generic function)
(setf cooling-factor) (generic function)
Divisor to compute edge forces. Can also be set per edge via data.
:edge-elasticity
32
edge-elasticity (generic function)
(setf edge-elasticity) (generic function)
Ideal edge (non nested) length. Can also be set per edge via data.
:ideal-edge-length
32
ideal-edge-length (generic function)
(setf ideal-edge-length) (generic function)
Initial temperature (maximum node displacement)
:initial-temp
1000.0d0
initial-temp (generic function)
(setf initial-temp) (generic function)
Lower temperature threshold (below this point the layout will end)
:min-temp
1.0d0
min-temp (generic function)
(setf min-temp) (generic function)
Node repulsion (overlapping) multiplier
:node-overlap
4
node-overlap (generic function)
(setf node-overlap) (generic function)
Node repulsion (non overlapping) multiplier. Can also be set per node in data.
:node-repulsion
2048
node-repulsion (generic function)
(setf node-repulsion) (generic function)
Initarg | Value |
---|---|
:%model-name | "coselayoutmodel" |
:%view-name | "coselayoutview" |
:refresh | 10 |
cytoscape.lisp (file)
dom-widget (class)
A minimum bound on the zoom level of the graph. The viewport can not be scaled smaller than this zoom level.
:min-zoom
1.0d-50
min-zoom (generic function)
(setf min-zoom) (generic function)
A maximum bound on the zoom level of the graph. The viewport can not be scaled larger than this zoom level.
:max-zoom
1.0d50
max-zoom (generic function)
(setf max-zoom) (generic function)
Whether zooming the graph is enabled, both by user events and programmatically.
:zooming-enabled
t
zooming-enabled (generic function)
(setf zooming-enabled) (generic function)
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.
:user-zooming-enabled
t
user-zooming-enabled (generic function)
(setf user-zooming-enabled) (generic function)
Whether panning the graph is enabled, both by user events sand programmatically.
:panning-enabled
t
panning-enabled (generic function)
(setf panning-enabled) (generic function)
Whether user events (e.g. dragging the graph background) are
allowed to pan the graph. Programmatic changes to pan are unaffected by
this option.
:panning-enabled
t
user-panning-enabled (generic function)
(setf user-panning-enabled) (generic function)
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.
:box-selection-enabled
t
box-selection-enabled (generic function)
(setf box-selection-enabled) (generic function)
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).
:selection-type
"single"
selection-type (generic function)
(setf selection-type) (generic function)
A non-negative integer that indicates the maximum allowable distance that a user may move during a tap gesture
:touch-tap-threshold
8
touch-tap-threshold (generic function)
(setf touch-tap-threshold) (generic function)
A non-negative integer that indicates the maximum allowable distance that a user may move during a tap gesture
:desktop-tap-threshold
4
desktop-tap-threshold (generic function)
(setf desktop-tap-threshold) (generic function)
Whether nodes should be locked (not draggable at all) by default (if true, overrides individual node state).
:autolock
autolock (generic function)
(setf autolock) (generic function)
Whether nodes should be ungrabified (not grabbable by user) by default (if true, overrides individual node state).
:auto-ungrabify
auto-ungrabify (generic function)
(setf auto-ungrabify) (generic function)
Whether nodes should be unselectified (immutable selection state) by default (if true, overrides individual element state).
:auto-unselectify
auto-unselectify (generic function)
(setf auto-unselectify) (generic function)
A convenience option that initialises the instance to run headlessly.
:headless
headless (generic function)
(setf headless) (generic function)
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.
:style-enabled
t
style-enabled (generic function)
(setf style-enabled) (generic function)
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.
:hide-edges-on-viewport
hide-edges-on-viewport (generic function)
(setf hide-edges-on-viewport) (generic function)
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.
:texture-on-viewport
texture-on-viewport (generic function)
(setf texture-on-viewport) (generic function)
A rendering hint that when set to t makes the renderer
use a motion blur effect to make the transition between frames seem smoother.
:motion-blur
motion-blur (generic function)
(setf motion-blur) (generic function)
When motionBlur: t, this value controls the opacity of motion blur frames.
:motion-blur-opacity
0.2
motion-blur-opacity (generic function)
(setf motion-blur-opacity) (generic function)
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).
:wheel-sensitivity
1.0
wheel-sensitivity (generic function)
(setf wheel-sensitivity) (generic function)
Layout algorithms
:graph-layouts
graph-layouts (generic function)
(setf graph-layouts) (generic function)
The stylesheet for the graph
:graph-style
graph-style (generic function)
(setf graph-style) (generic function)
Pan location of the graph.
:pan
(list (cons :x 0) (cons :y 0))
pan (generic function)
(setf pan) (generic function)
Zoom level of the graph.
:zoom
1.0
zoom (generic function)
(setf zoom) (generic function)
Field name in data of the tooltips.
:tooltip-source
"tooltip"
tooltip-source (generic function)
(setf tooltip-source) (generic function)
The list of graph elements
:elements
elements (generic function)
(setf elements) (generic function)
The context menus for the graph
:context-menus
context-menus (generic function)
(setf context-menus) (generic function)
Initarg | Value |
---|---|
:%model-name | "cytoscapemodel" |
:%model-module | cytoscape::+module-name+ |
:%model-module-version | cytoscape::+module-version+ |
:%view-name | "cytoscapeview" |
:%view-module | cytoscape::+module-name+ |
:%view-module-version | cytoscape::+module-version+ |
Dagre graph layout algorithm.
graph-layout.lisp (file)
the separation between adjacent edges in the same rank
:edge-sep
:null
edge-sep (generic function)
(setf edge-sep) (generic function)
Higher weight edges are generally made shorter and straighter than lower weight edges. Can also be set per edge via data.
:edge-weight
1
edge-weight (generic function)
(setf edge-weight) (generic function)
Number of ranks to keep between the source and target of the edge. Can also be set per edge via data.
:min-length
1
min-length (generic function)
(setf min-length) (generic function)
the separation between adjacent nodes in the same rank
:node-sep
:null
node-sep (generic function)
(setf node-sep) (generic function)
’TB’ for top to bottom flow, ’LR’ for left to right,
:rank-dir
:null
rank-dir (generic function)
(setf rank-dir) (generic function)
Type of algorithm to assign a rank to each node in the input graph. Possible values: ’network-simplex’, ’tight-tree’ or ’longest-path’
:ranker
:null
ranker (generic function)
(setf ranker) (generic function)
the separation between each rank in the layout
:rank-sep
:null
rank-sep (generic function)
(setf rank-sep) (generic function)
Initarg | Value |
---|---|
:%model-name | "dagrelayoutmodel" |
:%view-name | "dagrelayoutview" |
A node or an edge in a graph.
cytoscape.lisp (file)
widget (class)
Element type. Must be either nodes or edges.
:group
"nodes"
group (generic function)
(setf group) (generic function)
T if the element has been removed from the graph.
:removed
removed (generic function)
(setf removed) (generic function)
Whether the element is selected in the graph.
:selected
selected (generic function)
(setf selected) (generic function)
T if the element can be selected.
:selectable
t
selectable (generic function)
(setf selectable) (generic function)
T if the element will not be moved during a layout.
:locked
locked (generic function)
(setf locked) (generic function)
T if if the element is currently grabbed.
:grabbed
grabbed (generic function)
(setf grabbed) (generic function)
T if the element can be grabbed.
:grabbable
t
grabbable (generic function)
(setf grabbable) (generic function)
A list of CSS classes
:classes
classes (generic function)
(setf classes) (generic function)
An alist of the properties of the element.
:data
data (generic function)
(setf data) (generic function)
The position of the element.
:position
%position (generic function)
(setf %position) (generic function)
Initarg | Value |
---|---|
:%model-name | "elementmodel" |
:%model-module | cytoscape::+module-name+ |
:%model-module-version | cytoscape::+module-version+ |
:%view-name | "elementview" |
:%view-module | cytoscape::+module-name+ |
:%view-module-version | cytoscape::+module-version+ |
fCoSE graph layout algorithm.
graph-layout.lisp (file)
Layout quality
:quality
"default"
quality (generic function)
(setf quality) (generic function)
Whether or not simple nodes (non-compound nodes) are of uniform dimensions
:uniform-node-dimensions
uniform-node-dimensions (generic function)
(setf uniform-node-dimensions) (generic function)
Whether to pack disconnected components - valid only if randomize: true
:pack-components
t
pack-components (generic function)
(setf pack-components) (generic function)
False for random, true for greedy sampling
:sampling-type
t
sampling-type (generic function)
(setf sampling-type) (generic function)
Sample size to construct distance matrix
:sample-size
25
sample-size (generic function)
(setf sample-size) (generic function)
Separation amount between nodes
:node-separation
75
node-separation (generic function)
(setf node-separation) (generic function)
Power iteration tolerance
:pi-tol
1.0e-7
pi-tol (generic function)
(setf pi-tol) (generic function)
Node repulsion (non overlapping) multiplier
:node-repulsion
4500
node-repulsion (generic function)
(setf node-repulsion) (generic function)
Ideal edge (non nested) length
:ideal-edge-length
50
ideal-edge-length (generic function)
(setf ideal-edge-length) (generic function)
Divisor to compute edge forces
:edge-elasticity
0.45
edge-elasticity (generic function)
(setf edge-elasticity) (generic function)
For enabling tiling
:tile
t
tile (generic function)
(setf tile) (generic function)
Represents the amount of the vertical space to put between the zero degree members during the tiling operation(can also be a function)
:tile-padding-vertical
10
tile-padding-vertical (generic function)
(setf tile-padding-vertical) (generic function)
Represents the amount of the horizontal space to put between the zero degree members during the tiling operation(can also be a function)
:tile-padding-horizontal
10
tile-padding-horizontal (generic function)
(setf tile-padding-horizontal) (generic function)
Gravity range (constant) for compounds
:gravity-range-compound
1.5d0
gravity-range-compound (generic function)
(setf gravity-range-compound) (generic function)
Gravity range (constant)
:gravity-range
3.8d0
gravity-range (generic function)
(setf gravity-range) (generic function)
Gravity force (constant) for compounds
:gravity-compound
1.0d0
gravity-compound (generic function)
(setf gravity-compound) (generic function)
Initial cooling factor for incremental layout
:initial-energy-on-incremental
0.3d0
initial-energy-on-incremental (generic function)
(setf initial-energy-on-incremental) (generic function)
Initarg | Value |
---|---|
:%model-name | "fcose_layoutmodel" |
:%view-name | "fcose_layoutview" |
:nesting-factor | 0.1d0 |
:num-iter | 2500 |
:gravity | 0.25d0 |
:randomize | t |
Graph layout algorithm.
graph-layout.lisp (file)
widget (class)
Elements that the layout applies to.
:selector
"*"
selector (generic function)
(setf selector) (generic function)
:on-layout-stop
%on-layout-stop (generic function)
(setf %on-layout-stop) (generic function)
Initarg | Value |
---|---|
:%model-name | "graphlayoutmodel" |
:%model-module | cytoscape::+module-name+ |
:%model-module-version | cytoscape::+module-version+ |
:%view-name | "graphlayoutview" |
:%view-module | cytoscape::+module-name+ |
:%view-module-version | cytoscape::+module-version+ |
Grid graph layout algorithm.
graph-layout.lisp (file)
Extra spacing around nodes when avoidOverlap: true
:avoid-overlap-padding
10
avoid-overlap-padding (generic function)
(setf avoid-overlap-padding) (generic function)
Force num of cols in the grid
:cols
:null
cols (generic function)
(setf cols) (generic function)
Uses all available space on false, uses minimal space on true
:condense
condense (generic function)
(setf condense) (generic function)
Force num of rows in the grid
:rows
:null
rows (generic function)
(setf rows) (generic function)
Initarg | Value |
---|---|
:%model-name | "gridlayoutmodel" |
:%view-name | "gridlayoutview" |
Menu commands and selection handlers for context menus.
context-menu.lisp (file)
widget (class)
Custom background color for item.
:fill-color
fill-color (generic function)
(setf fill-color) (generic function)
HTML/text content to be displayed in the menu.
:content
""
content (generic function)
(setf content) (generic function)
css key:value pairs to set the command’s css in js if you want.
:content-style
content-style (generic function)
(setf content-style) (generic function)
Whether the command is selectable.
:enabled
t
enabled (generic function)
(setf enabled) (generic function)
Selection handlers
:on-select
on-select (generic function)
(setf on-select) (generic function)
Initarg | Value |
---|---|
:%model-name | "menucommandmodel" |
:%model-module | cytoscape::+module-name+ |
:%model-module-version | cytoscape::+module-version+ |
:%view-name | "menucommandview" |
:%view-module | cytoscape::+module-name+ |
:%view-module-version | cytoscape::+module-version+ |
Null graph layout algorithm.
graph-layout.lisp (file)
graph-layout (class)
Initarg | Value |
---|---|
:%model-name | "nulllayoutmodel" |
:%view-name | "nulllayoutview" |
Preset graph layout algorithm.
graph-layout.lisp (file)
The pan level to set (prob want fit = false if set)
:pan
:null
pan (generic function)
(setf pan) (generic function)
The zoom level to set (prob want fit = false if set)
:zoom
:null
zoom (generic function)
(setf zoom) (generic function)
Initarg | Value |
---|---|
:%model-name | "presetlayoutmodel" |
:%view-name | "presetlayoutview" |
Random graph layout algorithm.
graph-layout.lisp (file)
Initarg | Value |
---|---|
:%model-name | "randomlayoutmodel" |
:%view-name | "randomlayoutview" |
Previous: Exported definitions, Up: Definitions [Contents][Index]
• Internal special variables | ||
• Internal generic functions | ||
• Internal classes |
Next: Internal generic functions, Previous: Internal definitions, Up: Internal definitions [Contents][Index]
version.lisp (file)
version.lisp (file)
Next: Internal classes, Previous: Internal special variables, Up: Internal definitions [Contents][Index]
The position of the element.
cytoscape.lisp (file)
Selection handlers
context-menu.lisp (file)
space-separated cytoscape events that will open the menu; only ‘cxttapstart‘ and/or ‘taphold‘ work here
context-menu.lisp (file)
Previous: Internal generic functions, Up: Internal definitions [Contents][Index]
graph-layout.lisp (file)
standard-object (class)
Duration of animation in ms, if enabled
:animation-duration
250
animation-duration (generic function)
(setf animation-duration) (generic function)
Easing of animation, if enabled
:animation-easing
:null
animation-easing (generic function)
(setf animation-easing) (generic function)
graph-layout.lisp (file)
standard-object (class)
Prevents node overlap, may overflow boundingBox if not enough space
:avoid-overlap
t
avoid-overlap (generic function)
(setf avoid-overlap) (generic function)
graph-layout.lisp (file)
standard-object (class)
constrain layout bounds; { x1, y1, x2, y2 } or { x1, y1, w, h }
:bounding-box
:null
bounding-box (generic function)
(setf bounding-box) (generic function)
graph-layout.lisp (file)
standard-object (class)
Whether to animate changes to the layout
:animate
t
animate (generic function)
(setf animate) (generic function)
Whether to fit the viewport to the graph
:fit
t
fit (generic function)
(setf fit) (generic function)
Padding to leave between graph and viewport
:padding
30
padding (generic function)
(setf padding) (generic function)
graph-layout.lisp (file)
standard-object (class)
Gravity force (constant)
:gravity
1
gravity (generic function)
(setf gravity) (generic function)
graph-layout.lisp (file)
standard-object (class)
Nesting factor (multiplier) to compute ideal edge length for nested edges
:nesting-factor
1.2d0
nesting-factor (generic function)
(setf nesting-factor) (generic function)
graph-layout.lisp (file)
standard-object (class)
Includes the label when calculating node bounding boxes for the layout algorithm.
:node-dimensions-include-labels
node-dimensions-include-labels (generic function)
(setf node-dimensions-include-labels) (generic function)
graph-layout.lisp (file)
standard-object (class)
Maximum number of iterations to perform
:num-iter
1000
num-iter (generic function)
(setf num-iter) (generic function)
graph-layout.lisp (file)
standard-object (class)
Whether the layout should go clockwise (true) or counterclockwise/anticlockwise (false)
:clockwise
t
clockwise (generic function)
(setf clockwise) (generic function)
Where nodes start in radians
:start-angle
(* 3/2 pi)
start-angle (generic function)
(setf start-angle) (generic function)
How many radians should be between the first and last node (defaults to full circle)
:sweep
:null
sweep (generic function)
(setf sweep) (generic function)
graph-layout.lisp (file)
standard-object (class)
Use random node positions at beginning of layout
:randomize
randomize (generic function)
(setf randomize) (generic function)
graph-layout.lisp (file)
standard-object (class)
Number of ticks per frame; higher is faster but more jerky
:refresh
1
refresh (generic function)
(setf refresh) (generic function)
graph-layout.lisp (file)
standard-object (class)
Applies a multiplicative factor (>0) to expand or compress the overall area that the nodes take up
:spacing-factor
:null
spacing-factor (generic function)
(setf spacing-factor) (generic function)
Previous: Definitions, Up: Top [Contents][Index]
• Concept index | ||
• Function index | ||
• Variable index | ||
• Data type index |
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