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Using the Heatmap

There are two heatmap states that can be used on the molecular data page: Ranked Genes and Clustered Expression.

  • Ranked genes: displays the top genes according to DE calculations for a cell label or cluster. See Running Differential Expression for more information.
  • Clustered expression: displays the top genes clustered hierarchically by expression pattern for a selected set of cells. This can be used to analyze gene expression in broad clusters in order to break them in to subclusters.

Expanding and collapsing the heatmap view:

  1. The heatmap can be expanded by clicking the Enlarge Heatmap icon in the top right corner of the heatmap.
The heatmap with the Enlarge Heatmap icon highlighted.
  1. To expand the heatmap view further, click the < icon on the left side of the heatmap to collapse the left panel.
The expanded heatmap with the collapse left panel icon highlighted.
  1. Exit the expanded heatmap by clicking the Exit Enlarged View icon.
The expanded heatmap with the expand left panel and exit expanded view icons highlighted.

Setting the number of genes to display:

  1. The default number of genes displayed on the ranked genes heatmap is 3, the number can be set to any number between 1 and 9. To update the number of genes displayed click on the Settings Gear icon and enter the desired number of genes to display.
Heatmap with the settings gear highlighted.

Expanding the heatmap for a selected cluster:

  1. Select cluster or cell labels on the embedding or in the Sets of Cell Labels in the left panel. The selected cells will be colored red on the embedding and in the bar above the heatmap. The view of the selected cells can be expanded by clicking on the Expand Selection icon.
The heatmap with the expand selection icon highlighted.

Using the clustered expression heatmap:

  1. Select the cluster or cell label on the embedding or in Sets of Cell Labels. Once the cells have been selected, click on Clustered Expression on the heatmap to open the clustered expression heatmap.
The heatmap with clustered expression highlighted.