plot_peptideMods {PTXQC}

Plot peptide modification frequencies

Description

The input is a data.frame, as obtained from modsToTableByRaw().

Usage

plot_peptideMods(tbl, y_max = NA, show_missing_modification_levels = TRUE)

Arguments

tbl

A data.frame with 'fc.raw.file', 'modification_names' (can be a factor), and 'Freq' (0-100)

y_max

The upper limit of the y-axis's (==Freq); useful for multiple plots with identical limits; if 'NA' the limit is computed from the given 'tbl'

show_missing_modification_levels

If 'tbl$modification_names' is a factor and has more (but missing) levels than actually used, should missing values be dropped or assumed as '0' frequency?

Value

GGplot object

Examples

 data = data.frame(fc.raw.file = rep(c("file A", "file B"), each=3),
                   modifications = c("Oxidation (M)",
                   "Unmodified",
                   "Oxidation (M), Acetyl (Protein N-term)",
                   "2 Oxidation (M)", 
                   "Unmodified", 
                   "Unmodified"))
 tbl = modsToTableByRaw(data)
 plot_peptideMods(tbl,show_missing_modification_levels = TRUE)