plot_frequency: Plot protein overlap between samples

In DEP: Differential Enrichment analysis of Proteomics data

Description

plot_frequency generates a barplot of the protein overlap between samples

Usage

plot_frequency(se, plot = TRUE)

Arguments

se	SummarizedExperiment, Data object for which to plot observation frequency.
plot	Logical(1), If TRUE (default) the barplot is produced. Otherwise (if FALSE), the data which the barplot is based on are returned.

Value

Barplot of overlap of protein identifications between samples (generated by ggplot)

Examples

# Load example
data <- UbiLength
data <- data[data$Reverse != "+" & data$Potential.contaminant != "+",]
data_unique <- make_unique(data, "Gene.names", "Protein.IDs", delim = ";")

# Make SummarizedExperiment
columns <- grep("LFQ.", colnames(data_unique))
exp_design <- UbiLength_ExpDesign
se <- make_se(data_unique, columns, exp_design)

# Filter and plot frequency
filt <- filter_missval(se, thr = 0)
plot_frequency(filt)

DEP documentation built on Nov. 8, 2020, 7:49 p.m.