Plot protein overlap between samples — plot

plot_frequency generates a barplot of the protein overlap between samples

Usage

plot_frequency(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 overlap of protein identifications between samples (generated by ggplot)

Examples

# Load example
data(Silicosis_pg)
data_unique <- make_unique(Silicosis_pg, "Gene.names", "Protein.IDs", delim = ";")
# Make SummarizedExperiment
ecols <- grep("LFQ.", colnames(data_unique))
se <- make_se_parse(data_unique, ecols, mode = "delim", sep = "_")

# Filter and plot frequency
filt <- filter_se(se, thr = 0, fraction = 0.3)
#> filter base on missing number is <= 0 in at least one condition.
#> filter base on missing number fraction < 0.3 in each row

plot_frequency(filt)