plot_coverage: Plot protein coverage

Description Usage Arguments Value Examples

View source: R/plot_functions_frequencies.R

Description

plot_coverage generates a barplot of the protein coverage in all 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 protein coverage in 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 coverage
filt <- filter_missval(se, thr = 0)
plot_coverage(filt)

squirrelandr/DEP documentation built on May 7, 2019, 9:31 a.m.