GEX_dottile_plot: GEX Dottile plots

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

GEX Dottile plots

Description

Outputs a dotplot for gene expression, where the color of each dot is scaled by the gene expression level and the size is scaled by the % of cells positive for the gene

Usage

GEX_dottile_plot(GEX, genes, group.by, threshold.to.plot, platypus.version)

Arguments

GEX	GEX seurat object generated with VDJ_GEX_matrix
genes	Character vector. Genes of those in rownames(GEX) to plot. Can be any number, but more then 30 is discuraged because of cluttering
group.by	Character. Name of a column in [e-mail] to split the plot by. If set to \"none\", a plot with a single column will be produced.
threshold.to.plot	Integer 1-100. % of cells which must be expressing the feature to plot a point. If below, the field will be left empty
platypus.version	This is coded for \"v3\" only, but in practice any Seurat Object can be fed in

Value

Returns a ggplot object were the dot size indicates the percentage of expressing cells and the dot color indicates the expression level.

Examples

try({GEX_dottile_plot(GEX = Platypus::small_vgm[[2]], genes = c("CD19","CD83"),
group.by = "seurat_clusters", threshold.to.plot = 5)})

Platypus documentation built on Oct. 18, 2024, 5:08 p.m.