plot_coverage {DEP}R Documentation

Plot protein coverage

Description

plot_coverage generates a barplot of the protein coverage in all samples.

Usage

plot_coverage(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 protein coverage in 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 coverage
filt <- filter_missval(se, thr = 0)
plot_coverage(filt)

[Package DEP version 1.14.0 Index]