sampleStyles.xml
file inthe sampleData directory. You can import the sample file from File →Import → Styles from File….Node Properties | Description |
---|---|
Border Line Type | The type of line used for the border of the node. |
Border Transparency | The opacity of the color of the border of the node. Zero means totally transparent, and 255 means totally opaque. |
Border Width | The width of the node border. |
Label | The text used for the node label. |
Label Font Face | The font used for the node label. |
Label Font Size | The size of the font used for the node label. |
Label Position | The position of the node label relative to the node. |
Label Transparency | The opacity of the node label. Zero means totally transparent, and 255 means totally opaque. |
Label Width | The maximum width of the node label. If the node label is wider than the specified width, Cytoscape will automatically wrap the label on space characters. Cytoscape will not hyphenate words, meaning that if a single word (i.e. no spaces) is longer than maximum width, the word will be displayed beyond the maximum width. |
Nested Network Image Visible | A boolean value that indicates whether a nested network should be visualized (assuming a nested network is present for the specified node). |
Padding (Compound Node) | Internal padding of the compound node (a node that contains other nodes). |
Paint | The color of the whole node, including its border, label and selected paint. This property can be added to the list from the drop-down menu Properties → Paint → Paint. |
Border Paint | The color of the border of the node. This property can be added to the list from the drop-down menu Properties → Paint → Border Paint. |
Image/Chart 1-9 | A user-defined graphic (image, chart or gradient) that is displayed on the node. These properties (maximum of nine) can be added to the list from the drop-down menu Properties → Paint → Custom Paint n → Image/Chart n. |
Image/Chart Position 1-9 | The position of each graphic (image, chart or gradient). These properties (maximum of nine) can be added to the list from the drop-down menu Properties → Paint → Custom Paint n → Image/Chart Position n. |
Fill Color | The color of the node. This property can be added to the list from the drop-down menu Properties → Paint → Fill Color. |
Label Color | The color of the node label. This property can be added to the list from the drop-down menu Properties → Paint → Label Color. |
Selected Paint | The fill color of the node when selected. This property can be added to the list from the drop-down menu Properties → Paint → Selected Paint. |
Shape | The shape of the node. |
Shape (Compound Node) | The shape of the compound node (a node that contains other nodes). |
Size | The size of the node. Width and height will be equal. This property is mutually exclusive of Node Height and Node Width. It can be added to the list from the drop-down menu Properties → Size → Size. |
Image/Chart Size 1-9 | The size of the related node Image/Chart. It can be added to the list from the drop-down menu Properties → Size → Image/Chart Size n. |
Height | The height of the node. Height will be independent of width. This property is mutually exclusive of Node Size. It can be added to the list from the drop-down menu Properties → Size → Height. |
Width | The width of the node. Width will be independent of height. This property is mutually exclusive of Node Size. It can be added to the list from the drop-down menu Properties → Size → Width. |
Fit Custom Graphics to node | Toggle to fit Image/Chart size to node size. It can be added to the list from the drop-down menu Properties → Size → Fit Custom Graphics to node. |
Lock node width and height | Toggle to ignore Width and Height, and to use Size for both values. It can be added to the list from the drop-down menu Properties → Size → Lock node width and height. |
Tooltip | The text of the tooltip that appears when a mouse hovers over the node. |
Transparency | The opacity of the color of the node. Zero means totally transparent, and 255 means totally opaque. |
Visible | Hides the node if set to false. By default, this value is set to true. |
X Location | X location of the node. Default value of this will be ignored. The value will be used only when mapping function is defined. |
Y Location | Y location of the node. Default value of this will be ignored. The value will be used only when mapping function is defined. |
Z Location | Z location of the node. Default value of this will be ignored. The value will be used only when mapping function is defined. |
Edge Properties | Description |
---|---|
Bend | The edge bend. Defines how the edge is rendered. Users can add multiple handles to define how to bend the edge line. |
Curved | If Edge Bend is defined, edges will be rendered as straight or curved lines. If this value is set to true, edges will be drawn as curved lines. |
Label | The text used for the edge label. |
Label Font Face | The font used for the edge label. |
Label Font Size | The size of the font used for the edge label. |
Label Transparency | The opacity of the color of the edge label. Zero means totally transparent, and 255 means totally opaque. |
Line Type | The type of stoke used to render the line (solid, dashed, etc.) |
Paint | The color of the whole edge (including the stroke and arrows) when it is selected or unselected. This property can be added to the list from the drop-down menu Properties → Paint → Paint. |
Color (Selected) | The color of the whole edge (stroke and arrows) when selected. This property can be added to the list from the drop-down menu Properties → Paint → Color (Selected) → Color (Selected). |
Source Arrow Selected Paint | The selected color of the arrow on the source node end of the edge. It can be added to the list from the drop-down menu Properties → Paint → Color (Selected) → Source Arrow Selected Paint. |
Stroke Color (Selected) | The color of the edge line when selected. It can be added to the list from the drop-down menu Properties → Paint → Color (Selected) → Stroke Color (Selected). |
Target Arrow Selected Paint | The selected color of the arrow on the target node end of the edge. It can be found in the drop-down menu Properties → Paint → Color (Selected) → Target Arrow Selected Paint. |
Color (Unselected) | The color of the whole edge (stroke and arrows) when it is not selected. It can be found in the drop-down menu Properties → Paint → Color (Unselected) → Color (Unselected). |
Source Arrow Unselected Paint | The color of the arrow on the source node end of the edge. It can be found in the drop-down menu Properties → Paint → Color (Unselected) → Source Arrow Unselected Paint. |
Stroke Color (Unselected) | The color of the edge line. It can be found in the drop-down menu Properties → Paint → Color (Unselected) → Stroke Color (Unselected). |
Target Arrow Unselected Paint | The color of the arrow on the target node end of the edge. It can be found in the drop-down menu Properties → Paint → Color (Unselected) → Target Arrow Unselected Paint. |
Label Color | The color of the edge label. It can be found in the drop-down menu Properties → Paint → Label Color. |
Source Arrow Shape | The shape of the arrow on the source node end of the edge. |
Target Arrow Shape | The shape of the arrow on the target node end of the edge. |
Tooltip | The text of the tooltip that appears when a mouse hovers over the edge. |
Transparency | The opacity of the of the edge. Zero means totally transparent, and 255 means totally opaque. |
Visible | Hides the edge if set to false. By default, this value is set to true. |
Width | The width of the edge line. |
Edge color to arrows | If true then Color (Unselected) is used for the whole edge, including its line and arrows. It can be found in the drop-down menu Properties → Paint → Color (Unselected) → Edge color to arrows. |
Network Properties | Description |
---|---|
Background Paint | The background color of the network view. |
Center X Location | The X location of network view center. |
Center Y Location | The Y location of network view center. |
Annotation Selection | Whether or not annotations are selectable. If this is false, users cannot select annotations. Avoid changing this property directly through the Style panel. |
Edge Selection | Whether or not edges are selectable. If this is false, users cannot select edges. Avoid changing this property directly through the Style panel. |
Node Selection | Whether or not nodes are selectable. If this is false, users cannot select nodes. Avoid changing this property directly through the Style panel. |
Node Label Selection | Whether or not node labels can be selected and repositioned manually. Avoid changing this property directly through the Style panel. |
Force High Detail | The Level of Detail policy for a network view. If this is true, the view elements will always be rendered in high detail. If false, Cytoscape will choose when it's best to lower the level of detail to improve performance. |
Scale Factor | The zoom level of the network view. |
Size | The size (width and height) of the network view. It can be found in the drop-down menu Properties → Size → Size. |
Height | The height of the network view. It can be found in the drop-down menu Properties → Size → Height. |
Width | The width of the network view. It can be found in the drop-down menu Properties → Size → Width. |
Title | The title of the network view. |
Available Shapes and Line Styles | Sample |
---|---|
Node Shapes | |
Line Types | |
Arrow Shapes |
Symbol | Description |
---|---|
- | Mapping is not supported for the specified property. |
+ | Mapping is fully supported for the specified property. |
o | Mapping is partially supported for the specified property. Support for 'continuous to continuous' mapping is not supported. |
Node Property | Passthrough Mapping | Discrete Mapping | Continuous Mapping | |
---|---|---|---|---|
Color | Fill Color | + | + | + |
Transparency | + | + | + | |
Border Paint | + | + | + | |
Border Transparency | + | + | + | |
Label Color | + | + | + | |
Label Transparency | + | + | + | |
Numeric | Size/Width/Height | + | + | + |
Label Font Size | + | + | + | |
Border Width | + | + | + | |
Label Width | + | + | + | |
Padding (Compound Node) | + | + | + | |
Image/Chart Size | + | + | + | |
Other | Border Line Type | + | + | o |
Shape | + | + | o | |
Shape (Compound Node) | + | + | o | |
Label | + | + | o | |
Tooltip | + | + | o | |
Label Font Face | + | + | o | |
Label Position | - | + | o | |
Nested Network Image Visible | + | + | o | |
Image/Chart | o | + | o | |
Image/Chart Position | - | + | o |
Edge Property | Passthrough Mapping | Discrete Mapping | Continuous Mapping | |
---|---|---|---|---|
Color | Color | + | + | + |
Transparency | + | + | + | |
Target Arrow Color | + | + | + | |
Source Arrow Color | + | + | + | |
Label Color | + | + | + | |
Label Transparency | + | + | + | |
Numeric | Width | + | + | + |
Label Font Size | + | + | + | |
Label Width | + | + | + | |
Other | Line Type | + | + | o |
Bend | - | + | o | |
Curved | + | + | o | |
Source Arrow Shape | + | + | o | |
Target Arrow Shape | + | + | o | |
Label | + | + | o | |
Tooltip | + | + | o | |
Label Font Face | - | + | o |
CytoscapeConfiguration/images3
directoryYOUR_HOME_DIRECTORY/CytoscapeConfiguration/images3
.sampleData/galFiltered.sif
.sampleData/galFiltered.sif
.['Bet.Cent.','Closen.Cent','Clust.Coeff.','Topol.Coeff.']
.Editor Type | Supported Data Type | Properties |
---|---|---|
Color Gradient Editor | Color | node/edge/border/label colors |
Continuous-Continuous Editor | Numbers | size/width/transparency |
Continuous-Discrete Editor | All others | font/shape/text/graphics/position/etc. |
1 handle (no gradient) | 2 handles |
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session_syle.xml
file is saved in the session file. Thismeans that if you save your session, you will not lose your properties.No other style files are saved during normal operation.default_vizmap.xml
file to your CytoscapeConfiguration
directory (found in your homedirectory). These styles will then be loaded each time Cytoscape isstarted.styles.xml
(Cytoscape 3 format) file.Imported properties will supplement existing properties or overrideexisting ones if the properties have the same name. You can also specifya style file using the -V command line option. Properties loaded fromthe command line will override any default properties. Note that legacymenu, but not by command line.