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Using the t-SNE plot, cells can be classified based on clustering results or differences in gene and pathway expression. 

Classifying cells using the interactive t-SNE plot

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By default, each sample in a multi-sample data set is plotted on its own t-SNE. 

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Numbered figure captions
SubtitleText Viewing expression levels for an individual cell. The dots on the legend indicate the expression level of the selected cell. AnchorName Viewing expression levels for a cell

Classifying cells on single-sample t-SNE plot

Now that cells are colored by expression of a microglia/macrophage marker, CD14, and a oligodendrocyte marker, MOBP, we can classify any cell that does not fall into one of these two groups as malignant cells. Because t-SNE groups cells that are similar across the high-dimensional gene expression data, we will consider cells that form a group with CD14 or MOBP-expressing cells as same cell type, even if they do not express the marker gene.

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Classifying cells from multiple samples using the interactive multi-sample t-SNE plot

For some data sets, cell types can be distinguished when all samples can be visualized together on one t-SNE plot. We will use a t-SNE plot of all samples to classify microglia/macrophage and oligodendrocyte cell types. 

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