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

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t-SNE plot (individual sample)

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

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Classifying cells

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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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