Plot protein coverage — plot

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

Usage

plot_coverage(se, plot = TRUE, features_type = "features")

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.
features_type: Character(1), the type of features used in title, like 'proteins', 'genes', 'peptides', default is 'features'

Value

Barplot of protein coverage in samples (generated by ggplot)

Examples

# Load example
data(Silicosis_pg)
data <- Silicosis_pg
data_unique <- make_unique(data, "Gene.names", "Protein.IDs", delim = ";")

# Make SummarizedExperiment
ecols <- grep("LFQ.", colnames(data_unique))


## Load experiement design
data(Silicosis_ExpDesign)
exp_design <- Silicosis_ExpDesign
se <- make_se(data_unique, ecols, exp_design)

# Filter and normalize
filt <- filter_se(se, thr = 0, fraction = 0.4, filter_formula = ~ Reverse != "+" & Potential.contaminant!="+")
#> filter base on missing number is <= 0 in at least one condition.
#> filter base on missing number fraction < 0.4 in each row
#> filter base on giving formula 

plot_coverage(filt)