Using the Heatmap

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

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.
Marker Genes: displays a heatmap with the marker genes provided by the scientist(s) for the dataset.
Custom: displays a custom set of genes selected by the user.

The heatmap can be expanded by clicking the Enlarge Heatmap icon in the top right corner of the heatmap and the expanded view can be exited by clicking the same icon to return to the regular view.

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.

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.

To use the marker genes heatmap, click on More above the heatmap and then select Marker Genes. The heatmap will display the marker genes provided by the scientist(s) for each cell label with the corresponding cell label denoted by the color-coded bar on the edge of the heatmap.

To use the custom heatmap, click on More above the heatmap and then Custom. Next, select genes to add to the heatmap by clicking on the empty box next to the gene in the gene table or search for a specific gene of interest. Genes can be removed from the heatmap by clicking the checkmark next to the gene in the heatmap.