plot_numbers: Plot protein numbers

Description Usage Arguments Value Examples

View source: R/plot_functions_frequencies.R

Description

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

Usage

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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

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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 numbers
filt <- filter_missval(se, thr = 0)
plot_numbers(filt)

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