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Plot screen results

Source: R/plot_screen.r
plot_screen.Rd

Plot screen results

Usage

plot_screen(
  res,
  sample = NULL,
  links = TRUE,
  labs = TRUE,
  min_reads = 10,
  cap_fc = 8,
  p_sig = 0.05
)

Arguments

res

A results `data.frame` from `screen_calc()`

sample

Which library to plot (default: all)

Whether to draw arrows between ref and significant alt peptides

labs

Whether to label genes in less dense areas

min_reads

Minimum number of reads to show as points (default: 10)

cap_fc

Maximum amount of fold-change to limit values to

p_sig

Maximum adjusted p-value to consider significant (default: 0.05)

Value

A `ggplot2` object of the differential expression results

Examples

if (interactive()) {
    res = data.frame(baseMean=c(20, 30), log2FoldChange=c(-1, 1), padj=c(0.2, 0.05),
        gene_name=c("GENE1", "GENE1"), pep_type=c("ref", "alt"),
        bc_type=c("pat1", "pat1"), mut_id=c("GENE1_A1", "GENE1_A1"))
    plot_screen(res, links=FALSE, labs=FALSE)
}