In wguo-research/scCancer: A package for automated processing of single cell RNA-seq data in cancer

r h.i.r h.ii Cell interaction analysis

In order to analyze the ligand-receptor interactions between the various cell types in cancer micro-environment, we use a ligand-receptor database FANTOM5, and estimate the interaction scores among cell sets (the default is clusters).

The interaction scores between all ligand-receptor pairs and all cell sets can be found in the table file InteractionScore.txt.

Here is a plot showing the number of ligand-receptor paris with score larger than 0.1 among clusters. The size of point means the number of ligand-receptor paris with scores larger than 0.1. The color of point means the sum of the ligand-receptor pairs scores. To compare conveniently, the bottom subplot shows the predicted cell type fraction of each cell set.

grid::grid.draw(results$inter.plot)

(Hi-res image: view)

Following are the top 10 scores ligand-receptor pairs.

format(head(results$interaction.score, 10), digits = 4)

h.ii <- h.ii + 1

wguo-research/scCancer documentation built on May 26, 2024, 9:12 p.m.