plot_numbers {DEP}R Documentation

Plot protein numbers

Description

plot_numbers generates a barplot of the number of identified proteins per sample.

Usage

plot_numbers(se, plot = TRUE)

Arguments

se

SummarizedExperiment, Data object for which to plot protein numbers (output from make_se() or make_se_parse()).

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 the number of identified proteins per sample (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 numbers
filt <- filter_missval(se, thr = 0)
plot_numbers(filt)

[Package DEP version 1.16.0 Index]