Platypus (version 3.6.0)

GEX_dottile_plot: 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)

Value

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

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

Examples

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