psmplot: Visualize control PSMs versus test PSMs on a log-log plot.

In rachaelcox/enrichr: Compute Protein Enrichment

Description

Graphs control PSMs versus test PSMs on a log-log plot. A pseudocount of 1 is adding to all PSMs for log-log visualization. Colored by Z-test threshold. See README for file formats and example usage on the enrichr GitHub Repository.

Usage

psmplot(
  data,
  outfile_prefix,
  threshold,
  num_labs,
  label_file,
  ylab,
  xlab,
  point_color
)

Arguments

data	A data frame produced by enrich().
outfile_prefix	Optional. File prefix for output .png and .pdf files. Default = "output."
threshold	Optional. FDR threshold to color points by. One of c(90, 95, 99). Default = 5% FDR (fdr_bh <= 0.05).
num_labs	Optional. Number of annotation labels to display. Requires input to have an annotation column named gene_names_primary. Default = 0.
label_file	Optional. Comma-separated file containing names of genes to be labeled on the plot; requires input to have an annotation column named gene_names_primary and labels must match format in the column.
ylab	Text for y-axis label; will correspond to test PSMs.
xlab	Text for x-axis label; will correspond to control PSMs.

Value

PSM log-log plots in .png and .pdf format.

rachaelcox/enrichr documentation built on Jan. 19, 2021, 2:11 p.m.