Bar chart subtypes: Grouped, Stacked, Heat Strips and Up-Downįor more detailed information on how to use Custom Graphics, see the Cytoscape Manual.There are several other graphics available through the default Custom Graphics in Cytoscape: Add the Image/Chart Position 3 property and position the chart to the left of the node.Keep the rest of the settings default and click Apply.Define a Pie Chart with the Radiality and Degree columns.Add a third Custom Graphic under Paint → Custom Paint → Image/Chart 3.The nodes in your network should now look like this: Custom Graphics Pie Chartįinally, we will create a pie chart with two columns, Radiality and Degree. Select the Cyan-White-Yellow color scheme.įor the heatmap, we can keep the default placement.Under Customize, select Horizontal Orientation.Again, select the three columns containing expression data gal1RGexp, gal4RGexp and gal80Rexp, and remove any other columns selected by default. Under Charts select Heatmap option (third icon from the left).Add another Custom Graphic by selecting Paint → Custom Paint → Image/Chart 2 from the Properties drop-down menu.Next we are going to create a horizontal heatmap of the same three data columns. The nodes in your network should now look like this: Custom Graphics Heatmap You may have to adjust this positioning a few times to achieve an optimal visualization. Drag the darker blue Object to right below the node.column of this new entry to bring up a position editor. To move it, select Paint → Custom Paint → Image/Chart Position 1 from the Properties drop-down menu. The chart is now centered on the node.Under ColorBrewer Qualitative, select the Paired colors palette (light blue/blue/green). Expand the Customize section and click the Color Palette button.You may need to remove columns selected by default from the Selected Columns list, this should only list our three columns of interest. In the Available Columns list, select the three columns with expression data: gal1RGexp, gal4RGexp and gal80Rexp.We are going to use the default selected graph type, Grouped Bar Chart.In the Graphics interface, select the Charts tab.In the Style interface, click on default ( Def.) for the Image/Chart 1 property.In this example, we will create a bar chart with the three expression values, gal1RGexp, gal4RGexp and gal80Rexp, available as attributes in the session file. The nodes are labeled with yeast ORF identifiers. Switch the default node Fill Color to a light grey.In the Style interface, switch to the default style in the drop-down at the top.Launch Cytoscape and open the Yeast Perturbation session file from the Cytoscape Starter Panel.For this tutorial, we will be using the Yeast Perturbation sample session in the Cytoscape Starter Panel.
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