plot_ibaq: Plot iBAQ values versus log fold change

In arnesmits/DEPstoi: Stoichiometry analysis of label-free proteomics data

Description

plot_ibaq plots a scatter plot of the iBAQ intensities versus the LFQ fold changes.

Usage

plot_ibaq(dep, contrast, labelsize = 3)

Arguments

dep	SummarizedExperiment object, Proteomics dataset on which differential enriched proteins are annotated by add_rejections.
contrast	Character(1), The specific contrast to plot.
labelsize	Integer(1), Sets the size of name labels.

Value

A scatter plot

Examples

# load data
proteins <- GFPip
exp_design <- GFPip_ExpDesign

# Test for differential enriched proteins
se <- import_MaxQuant(proteins, exp_design,
    filter = c("Reverse", "Contaminant"))
processed <- process(se, fun = "MinProb")
dep <- analyze_dep(processed, 'control', 'WT', lfc = 4.5)

# Plot iBAQ vs LFQ plot
plot_ibaq(dep, 'GFP_vs_WT', labelsize = 3)

arnesmits/DEPstoi documentation built on May 3, 2019, 4:31 p.m.