plot_stoichiometry: Plot relative stoichiometries

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

Description

plot_stoichiometry plots a barplot of the relative stoichiometries.

Usage

plot_stoichiometry(protein_stoichiometry, thr = 0.01, max_y = NULL)

Arguments

protein_stoichiometry	Data.frame, Stoichiometry table generated by get_stoichiometry.
thr	Numerical(1), The stoichiometry threshold above which proteins will be plotted.
max_y	Numerical(1), The maximum scale of the y-axis.

Value

A barplot (generated by ggplot).

Examples

# load data
proteins <- GFPip
proteins <- data_unique <- make_unique(proteins, 'Gene.names', 'Protein.IDs')
exp_design <- GFPip_ExpDesign
peptides <- GFPip_pep

# 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)

# Merge iBAQ intensities of proteins that have shared peptides
ibaq <- merge_ibaq(data_unique, peptides)

# Calculate relative stoichiometry versus 'Suz12' in the 'GFP_vs_WT' contrast
stoi <- get_stoichiometry(dep, ibaq, contrast = 'GFP_vs_WT', bait = 'Suz12')

# Plot stoichiometry
plot_stoichiometry(stoi)

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