pairwiseVln

Source: R/comparisons_with_markers.R

Make a grid of violin plots with the mean expression of each cluster, for markers dataset 1 is the sample whose expression values will be plot, and dataset 2 is the sample whose cluster markers are used.

pairwiseVln(seurat1, markers, seurat2,
  sample_names = c(seurat1@project.name, seurat2@project.name),
  marker_col = "gene")

Arguments

seurat1

Seurat object for which to plot expression
markers

Data frame as returned by Seurat::FindAllMarkers()
seurat2

Seurat object from which cluster markers (markers) were defined
sample_names

(Optional) Character vector giving the names or ID of the two samples, used for axis labels, etc. Default: c(seurat1@project.name, seurat2@project.name)
marker_col

String specifying the column in the markers data frames which specifies the cluster. By default, Seurat calls this "gene" (the default here); in objects produced by the lab's pipeline, it may be called "external_gene_name".

Value

A ggplot object

Examples

pairwiseVln(pbmc, markers_pbmc, pbmc)