plot_genes: Plot gene variance distributions

Description Usage Arguments Details Value Examples

View source: R/utils.R

Description

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

Usage

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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

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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.