GEX_pairwise_DEGs: Wrapper for calculating pairwise differentially expressed...

In 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
)

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 indipendently of their p value. Can be used in combination with label.n.genes.
save.plot	Boolean. Defaults to True. Whether to save plots as appropriately named .png 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)

Platypus documentation built on Aug. 15, 2022, 9:08 a.m.