group_violin_plot: Violin plots of gene expression for clusters

In AllenInstitute/L5_VEN:

Violin plots of gene expression for clusters

Description

This function will generate plots similar to Figure 1c of Tasic, et al. (2015). Warning: this is currently only able to work with internally-supplied datasets (v1_data and v1_anno). Extension to user-supplied datasets will come soon.

Usage

group_violin_plot(genes = c("Hspa8", "Snap25", "Gad2", "Vip"),
  group_by = "cluster", clusters = 1:10, data_source, sort = F,
  logscale = F, showcounts = T, rotatecounts = F, fontsize = 7,
  labelheight = 25, max_width = 10)

Arguments

genes	A character vector containing gene symbols to be plotted
clusters	A numeric vector containing clusters to plot (for v1_anno, the range is 1:49)
data_source	A character object defining where the data is stored. Currently only works with "internal"
logscale	Logical object, determines if data is log scaled before plotting.
fontsize	numeric object, the font size (in pts) used to make the plot.
labelheight	numeric object, Percent of the plot height that should be used for the labels (0 to 100).

Value

a ggplot2 plot object

Examples

pottery_plot()

my_genes <- c("Ercc6","Ercc8","Trp53","Pgbd5")
my_clusters <- c(1,5,9,10,24,37)
pottery_plot(my_genes,my_clusters,logscale=T,fontsize=14)

AllenInstitute/L5_VEN documentation built on July 31, 2022, 6:32 p.m.