Advanced Visualization: Graphics

This short protocol reviews how to add graphics to nodes.

Adding Graphics to Nodes

Sometimes, we want to add graphics to nodes. This should be done very sparingly, using Cytoscape's built-in charts. This example uses the Yeast Perturbation example session file.

• Remove the Node Fill Color mapping and set the default node color to grey.
• In the Node tab of the Style panel, select Properties→Paint→Custom Paint 1→Image/Chart 1.
• To add a graphic to all nodes, click the Def. (default) column of the Image/Chart 1 property. To add a graphic to only selected nodes, select the nodes first and then click the Byp (bypass) column for Image/Chart 1 property.
• Select Charts at the top. This will bring up the Graphics panel:

Adding Graphics to Nodes

• Select the type of chart at the top, in this example we are using the Bar Chart.
• For bar charts, select the type of chart using the radio buttons. For this example, we are choosing Up-Down.
• Using the Add Selected and Remove Selected arrows, move the data columns you want to use for your chart to the Selected Columns list. In this example, we are using gal1RGExp and gal80RExp.
• Click the Customize tab, and in the Color Palette drop-down, select the ColorBrewer Diverging red-blue color palette.

Adding Graphics to Nodes

• To add axis to the chart, check the three buttons for Show Domain Axis, Show Range Axis and Show Zero Baseline.
• For Separation, enter 0.05. Click Apply.

Adding Graphics to Nodes

By default, the charts are placed in the middle of the node. We can adjust the placement of the chart using the Image/Chart potision 1 property.

Adding Graphics to Nodes

• Add the Image/Chart position 1 property to the list by selecting it in the Properties drop-down under Paint→Custom Paint 1→Image/Chart Position 1.
• Click the Def. (default) column and set the chart position to the right of the node.

enhancedGraphics

enhancedGraphics was implemented before Cytoscape charts were added to Cytoscape core. The format is not nearly as convenient, but allows for greater flexibility and specificity. Briefly, adding a chart using enhancedGraphics is done as follows:

• Create a new text column in the node table.
• Add the chart instructions to the new column, see the manual for details on chart instructions.
• Set up a visual style that uses the column you created as a passthrough mapping for one of the CustomGraphics styles.

For a detailed exmaple of enhancedGraphics, see the Custom Graphics and Labels protocol.