Before heatmap visualization, transcript counts were transformed to z-normalized transcripts per million (TPM). Genes (top to bottom) and cells (left to right) were ordered according to the strength of statistical association (FDR q) with respective assigned Gene-States and Cell-States. The tsne R package v0.1-3 was used for dimensionality reduction by t-distributed stochastic neighbor embedding (t-SNE). Modified parameters include k = 2 and seed = 1234. Input for t-SNE was z-normalized TPM values across genes with at least three transcript counts in three cells (n = 4914 genes). Gene expression overlay onto t-SNE visualization was also performed using z-normalized TPM values.

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