Getting Started: Scatterplot (tSNE or UMAP)

The Scatterplot visualization shows each cell in the dataset in a 2D plot, generated from either the tSNE or UMAP algorithms. By default, the dots (cells) are colored by their cell type assignment. At a glance, most cells in a single type are visually grouped together in tSNE space, but not all. Zoom in/out and pan to examine cell types of interest.

Click on a cell to highlight all cells of the same type.

Examine Gene Expression in tSNE space
To color the cells by expression of a gene, click the “Color By” menu near the top left of the screen.

Choose a gene that you already have on the heatmap, or search for a gene using gene symbol.

Alternatively, color the tSNE by gene expression directly from the Heatmap view. Click the gene symbol in the heatmap view, and choose Color t-SNE with expression of .image

Gene Expression Histogram
When the scatterplot is colored by gene expression, you can select a cell type to see a histogram of gene expression for all cells in that type.

Customize Visualization
Change the color map by clicking on the current selection in the bottom of the screen.