plot_coverage {DEP} | R Documentation

## Plot protein coverage

### Description

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

### Usage

    plot_coverage(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 protein coverage in samples (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 coverage
    filt <- filter_missval(se, thr = 0)
    plot_coverage(filt)

[Package DEP version 1.12.0 Index]