Supplementary Figure 9: tSNE for single cell ATAC-seq using chromVAR or peak-based strategies.
From: chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data
(a) tSNE performed for all cell types, (b) tSNE performed only on HL60, LMPP, Monocyte, and AML cells. When using correlation (Pearson or Correlation), one minus the correlation was used as a distance input into Rtsne. When using distance or PCA, counts were first normalized using the total counts in peaks for each cell. When using PCA + euclidean distance, we used the default settings for Rtsne, which performs PCA and uses the first 50 PCs to compute a distance matrix. For each method, the same perplexity (25) was used.
