GEX_pairwise_DEGs: Wrapper for calculating pairwise differentially expressed...

In alexyermanos/Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis

Wrapper for calculating pairwise differentially expressed genes

Description

Produces and saves a list of volcano plots with each showing differentially expressed genes between pairs groups. If e.g. seurat_clusters used as group.by, a plot will be generated for every pairwise comparison of clusters. For large numbers of this may take longer to run. Only available for platypus v3

Usage

GEX_pairwise_DEGs(
  GEX,
  group.by,
  min.pct,
  RP.MT.filter,
  label.n.top.genes,
  genes.to.label,
  save.plot,
  save.csv
)

Arguments

GEX	Output Seurat object of the VDJ_GEX_matrix function (VDJ_GEX_matrix.output[[2]])
group.by	Character. Defaults to "seurat_clusters" Column name of [e-mail] to use for pairwise comparisons. More than 20 groups are discuraged.
min.pct	Numeric. Defaults to 0.25 passed to Seurat::FindMarkers
RP.MT.filter	Boolean. Defaults to True. If True, mitochondrial and ribosomal genes are filtered out from the output of Seurat::FindMarkers
label.n.top.genes	Integer. Defaults to 50. Defines how many genes are labelled via geom_text_repel. Genes are ordered by adjusted p value and the first label.n.genes are labelled
genes.to.label	Character vector. Defaults to "none". Vector of gene names to plot independently of their p value. Can be used in combination with label.n.genes.
save.plot	Boolean. Defaults to False. Whether to save plots as appropriately named .png files
save.csv	Boolean. Defaults to False. Whether to save deg tables as appropriately named .csv files

Value

A nested list with out[[i]][[1]] being ggplot volcano plots and out[[i]][[2]] being source DEG dataframes.

Examples

GEX_pairwise_DEGs(GEX = Platypus::small_vgm[[2]],group.by = "sample_id"
,min.pct = 0.25,RP.MT.filter = TRUE,label.n.top.genes = 2,genes.to.label = c("CD24A")
,save.plot = FALSE, save.csv = FALSE)

alexyermanos/Platypus documentation built on Feb. 8, 2025, 1:22 p.m.