Fig. 3: Exploration of qPHATE and its branched genes revealed in the mCRC scRNAseq atlas.
From: q-Diffusion leverages the full dimensionality of gene coexpression in single-cell transcriptomics
a q-Diffused and original PHATE embeddings of the atlas cells. Plots are sized to their true aspect ratios. Cells are colored by their estimated local intrinsic dimensionality (LID), which highlights possible branching points. Branches are annotated in red. They are less clear in the original PHATE embedding. See Supplementary Results for a rigorous investigation. Major branch #1 had about ~19% of the cells, major branch #2 about ~9% of the cells, and the minor branch accounted for ~4% of the cells. Supplementary Fig. 3 provides details and further evidence for our approach on defining branches in the embedding. b Major branches #1& 2 were contrasted against each other to screen for genes that appear to drive the branching. Expressions of the top screened genes are displayed in this heatmap. c The scRNAseq embedding in a was translated to the clinical-trial patients by linear projection. Then the principal component of that embedding was discretized around its mean for downstream analysis as a putative biomarker.
