Question: Which genes are displayed in the Loupe Cell Browser heatmap? How can I export the list of genes displayed?
Answer: In Loupe Cell Browser (version 6.3.0), the software considers the top N genes for each cluster, sorted by log2 fold-change (by default N = 120/X, where X is the total number of clusters in current view). The heatmap is generated using hierarchical clustering with euclidean distance and average linkage. The number of top genes in display can be changed by clicking the menu icon in the upper right corner of the heatmap.
To export the heatmap to a .png image where the full list of genes will be displayed on the x-axis, one can click on the camera icon in the upper right corner of the heatmap. The heatmap is interactive in that users can also hover their mouse over the individual spots to identify which gene is represented and its log2 fold-change (displayed above: Reg4 with log2 fold-change = 7.911). As of version 6.3.0, there is no 1-click function to export the associated information for the subset of genes on heatmap.