peptideProfilePlot: plot log2 intensities of all peptides for one gene in...

In yafeng/DEqMS: a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.

plot log2 intensities of all peptides for one gene in different samples

Description

This function is to plot log2 intensities of all peptides for one gene in different samples.

Usage

peptideProfilePlot(dat, col=2, gene)

Arguments

dat	a data frame with peptide/psm log2 intensities
col	an integer indicates the column number where the gene protein id is. default is 2, asumming the gene/protein is in the second column
gene	an character indicates the gene name/id to be plotted

Value

return a ggplot2 object

Author(s)

Yafeng Zhu

Examples

library(ExperimentHub)
eh = ExperimentHub(localHub=TRUE)
query(eh, "DEqMS")
dat.psm = eh[["EH1663"]]

dat.psm.log = dat.psm
dat.psm.log[,3:12] =  log2(dat.psm[,3:12])
    
peptideProfilePlot(dat.psm.log,col=2,gene="TGFBR2")

yafeng/DEqMS documentation built on Nov. 29, 2024, 1:48 a.m.