plot_volcano: Generates a volcano plot from the output of append_ec_sites()

In devradiumking/maxabpp: Visualization of MaxQuant output for activity-based protein profiling experiments

Description

Generates a volcano plot from the output of append_ec_sites()

Usage

plot_volcano(
  LFQ_table_ec,
  x,
  y,
  xlim,
  ylim,
  label_col_name,
  pCutoff,
  FCcutoff,
  title,
  label_site_containing_peptides_only = FALSE
)

Arguments

LFQ_table_ec	a dataframe saved as the append_ec_sites() output
x	log2FC column name
y	-log10pvalue column name
xlim	a integer vector, such as c(-5, 5) for an x axis range of -5 to 5
ylim	a integer vector, such as c(0, 5) for an y axis range of 0 to 5
label_col_name	the input column name for labeling volcano plot data points such as "Gene.Names"
pCutoff	the p-Value cutoff on -log10 scale, for instance, use 1.3 for p-value = 0.05
FCcutoff	the fold change cutoff on log2 scale, for instance, use -1 for -2 fold change, Note for ABPP, we are only interested in negative fold change
title	a string as the title of the volcano plot
label_site_containing_peptides_only	a boolean. IF TRUE, label probe-modified peptides covering active sites, binding sites, or other sites. Default value = FALSE.

Value

a volcano plot

See Also

pairwise_LFQ append_ec_sites

devradiumking/maxabpp documentation built on May 31, 2020, 9:01 a.m.