plot_coverage: Plot protein coverage
In squirrelandr/DEP: Differential Enrichment analysis of Proteomics data

Description Usage Arguments Value Examples

View source: R/plot_functions_frequencies.R

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

1	plot_coverage(se, plot = TRUE)

`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.

Barplot of protein coverage in samples (generated by ggplot)

# 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)