Skip to main content
Fig. 3 | Genome Biology

Fig. 3

From: TraSig: inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data

Fig. 3

CSHMM and TraSig’s results on the liver organoid data. a Reconstructed trajectory for scRNA-Seq profiled at day 5, day 11, and day 17 from pluripotent stem cell (PSC)-derived multilineage human liver organoids generated as previously described [11]. CSHMM reconstructs a tree-structured trajectory that clusters cells to edges based on their expression patterns and relationship to the expression patterns of prior edges (Methods). Cells are colored by their cell type labels and are shown as dots ordered by their pseudotime assignment. DesLO, designer liver organoid; HL, hepatocyte-like cells; DL, ductal/cholangiocyte-like cells; SL, stellate-like cells; EC, endothelial-like cells; PL, progenitor-like cells; WT, wild type. b, c UMAP [13] visualizations for day 11 and day 17 cells, colored by cell type labels. d Heatmap for scores assigned by TraSig to cluster pairs containing cells sampled at the same time. e Sliding window expression for four example ligand-receptor pairs predicted to interact by TraSig

Back to article page