plot_genes {ccfindR} | R Documentation

## Plot gene variance distributions

### 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)

[Package ccfindR version 1.7.0 Index]