Extended Data Fig. 7: Differential cell type abundance.
From: Organization of the human intestine at single-cell resolution
a–c) Beeswarm plot showing the log-fold change between the three main regions of the small intestine and colon for groups of nearest neighbour cells from different cell type clusters in the stromal (a), immune (b), and epithelial (c) compartments computed with Milo. Significant changes are indicated in colour. d) Boxplots comparing the fraction of all cells in each sample composed of each cell type for samples from the colon, ileum, jejunum, and duodenum. e) Log2FC in abundance of each cell type between the regions listed on the y-axis as estimated with scCODA. Only significant results at an FDR of 0.05 are shown, with all nonsignificant differences plotted as white.
