dot-makeVolcano: Create a volcano plot

In Vitek-Lab/MSstats: Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

Create a volcano plot

Description

Create a volcano plot

Usage

.makeVolcano(
  input,
  label_name,
  log_base_FC,
  log_base_pval,
  x.lim,
  ProteinName,
  dot.size,
  y.limdown,
  y.limup,
  text.size,
  FCcutoff,
  sig,
  x.axis.size,
  y.axis.size,
  legend.size,
  log_adjp
)

Arguments

input	data.table
label_name	contrast label
log_base_FC	2 or 10
log_base_pval	2 or 10
ProteinName	for volcano plot only, whether display protein names or not. TRUE (default) means protein names, which are significant, are displayed next to the points. FALSE means no protein names are displayed.
dot.size	size of dots in volcano plot and comparison plot. Default is 3.
text.size	size of ProteinName label in the graph for Volcano Plot. Default is 4.
FCcutoff	for volcano plot or heatmap, whether involve fold change cutoff or not. FALSE (default) means no fold change cutoff is applied for significance analysis. FCcutoff = specific value means specific fold change cutoff is applied.
sig	FDR cutoff for the adjusted p-values in heatmap and volcano plot. level of significance for comparison plot. 100(1-sig)% confidence interval will be drawn. sig=0.05 is default.
x.axis.size	size of axes labels, e.g. name of the comparisons in heatmap, and in comparison plot. Default is 10.
y.axis.size	size of axes labels, e.g. name of targeted proteins in heatmap. Default is 10.
legend.size	size of legend for color at the bottom of volcano plot. Default is 7.

Vitek-Lab/MSstats documentation built on Nov. 4, 2024, 3:08 p.m.