get_volcanoplots: get_volcanoplots

In kuppal2/xmsPANDA: R Package for Biomarker Discovery, Network, and Data Exploratory Analysis

Description

Function to generate volcano plots

Usage

get_volcanoplots(xvec, yvec, up_or_down, maintext = "", ythresh = 0.05,
 y2thresh = NA, ylab, xlab, colorvec = c("darkblue", "red3"), 
col_seq = c("brown", "chocolate3", "orange3", "coral", "pink",
 "skyblue", "blue", "darkblue", "purple", "violet"), 
xincrement = 1, yincrement = 1, xthresh = 1, pchvec = c(21, 21),
 background.points.col = "gray50", bad.feature.index = NA)

Arguments

xvec	Vector with log2 fold change values for the x-axis.
yvec	Vector with values for the y-axis. eg: (-)log10 of p-values, VIP, loadings, regression coefficients.
up_or_down	Same as xvec.
maintext	Text for the plot title
ythresh	Y-axis threshold for significance or differential expression. eg: 3 for p=0.001; y=(-1)*log10(0.001) or 2 for VIP from PLS
y2thresh	Optional secondary Y-axis threshold for significance or differential expression. eg: 1.3 for p=0.05; y=(-1)*log10(0.05) or 1 for VIP from PLS
ylab	Y-axis label
xlab	X-axis label
colorvec	Vector of colors for representing up-regulation and down-regulation. eg: c("darkgreen", "firebrick1") In this case, features that are up-regulated in class A will have "darkgreen" color, and features that are up-regulated in class B will have "firebrick1" color.
xincrement	Window size for breaking the x-axis into different segments for visualization purposes. eg: 150
yincrement	Window size for breaking the y-axis into different segments for visualization purposes. eg: 1
xthresh	Absolute value of the threshold for log2 fold change. e.g. 0, 1, 2

Details

This function generates volcano plots.

Value

Volcano plot

Author(s)

Karan Uppal; [e-mail]

kuppal2/xmsPANDA documentation built on May 15, 2021, 5:48 a.m.