plot_genes: Plot gene variance distributions

In ccfindR: Cancer Clone Finder

Description

Gene variance to mean ratio and the number of expressing cells are plotted.

Usage

plot_genes(object, vmr = NULL, ncexpr = NULL, selected_genes = NULL,
  variable_genes = NULL, mode_genes = NULL, marker_genes = NULL,
  save.memory = FALSE, progress.bar = TRUE, log = "xy", cex = 0.5)

Arguments

object	Object containing count data
vmr	Variance to mean ratio (VMR)
ncexpr	Number of cells expressing each gene
selected_genes	Logical vector specifing genes selected
variable_genes	Logical vector specifing genes with high VMR
mode_genes	Logical vector specifying genes with nonzero modes
marker_genes	Logical vector specifying marker genes
save.memory	If TRUE, calculate VMR using slower method to save memory. Not used when gene lists are supplied.
progress.bar	Display progress bar for VMR calculation. Not used when gene lists are supplied.
log	Axis in log-scale, c('x','y','xy').
cex	Symbol size for genes (supplied to plot()).

Details

This function can be called separately or is also called within filter_genes by default. In the latter case, parameters other than object will have been already filled. If called separately with NULL gene lists, VMR is recalculated but gene selection is not done.

Value

NULL

Examples

set.seed(1)
s <- scNMFSet(matrix(stats::rpois(n=1200,lambda=3),40,30))
plot_genes(s)

ccfindR documentation built on Nov. 8, 2020, 5:12 p.m.