How do I make a heatmap? - Cytobank documentation

Note: If you've never made one before, we suggest you try out one of the tutorials and walkthroughs

Before you create the heatmap, you must have already: uploaded experiment files (or cloned those of another experiment); annotated your staining panels (channels); drawn your gates (created populations); and annotated any conditions, individuals, or other parameters that you want to use in your plots.
On the Illustration page, under "Plot Controls", select "Plot Type" "Heatmap". Make sure to select the appropriate channels for your heatmap in the "Channels" dimension. Click "Update Illlustration." Adjust the other dimensions as needed and click on "Update Illustration".
Because this is a heatmap, the "Plot Statistics" area on the left navigation bar is active. In the "Plot Statistics" area, you can select to create a heatmap of a particular statistic or normalize against an "Unstimulated" or control sample. Select "Fold" for equation and "First Row" (or whatever is appropriate) for control and click "Update Illustration".
A heatmap should appear in the illustration tab. The corresponding table of values will also be present under the heatmap and legend. This table can be exported as tab-delimited data by clicking on the "Export Table of Statistics" link in the left navigation menu bar.
Hovering the cursor over any square on a heatmap will display the underlying plot for that file. You can change the underlying plot type using the "Viewthrough Plot Type" select box. The specific "X" and "Y" axes can be set using the Plot Controls Section. You can also control the color scheme and size of the viewthrough plots there.
Once you are satisfied with the heatmap, you can save the illustration to get a persistent URL to share with others.
Export the heatmap by generating a PDF of your illustration. Alternatively, you can open the heatmap in a printview and copy and paste the image into a program of your choice.

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