plot_numbers: Plot protein numbers

In squirrelandr/DEP: Differential Enrichment analysis of Proteomics data

Description

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

Usage

plot_numbers(se, plot = TRUE)

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

# 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.