Molecular Data Page Overview
The Molecular Data page has several functions: creating new cell labels, running differential expression and viewing embeddings with gene expression values.
- Differential expression: Can be done using all other cells or a custom set of selected cells to use as a reference. Additionally, the default is to run differential expression with downsampling for faster speed but this can be modified to use all cells.
- Clustered heatmap: Displays the top 3 genes per cluster with the color-coded bar above the heatmap indicating the cluster. The number of genes displayed can be modified and the source of the cluster can be set to either cell label or cluster using the buttons directly above the heatmap. An expanded view can be accessed using the button in the top right section of the heatmap.
- Gene table: Displays the highly variable genes and the differential expression results after running differential expression. The buttons to the left of each gene control the display of gene expression on the embedding and visibility in the heatmap.
- Embedding: If the dataset contains more than one embedding, you can select the embedding to display using the dropdown box in the bottom left part of the embedding, as well as adjust the zoom and download the embedding.
- Cell labels: Existing cell labels can be edited and new cell label annotations with associated cell metadata can be created in edit mode.