plot_frequency: Plot protein overlap between samples

Description Usage Arguments Value Examples

View source: R/plot_functions_frequencies.R

Description

plot_frequency generates a barplot of the protein overlap between samples

Usage

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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

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# 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)

arnesmits/DEP documentation built on Aug. 7, 2019, 10:44 a.m.