plot_single {DEP} | R Documentation

## Plot values for a protein of interest

### Description

`plot_single` generates a barplot of a protein of interest.

### Usage

    plot_single(dep, proteins, type = c("contrast", "centered"), plot = TRUE)

### Arguments

`dep` | SummarizedExperiment, Data object for which differentially enriched proteins are annotated (output from `test_diff()` and `add_rejections()`).
`proteins` | Character, The name(s) of the protein(s) to plot.
`type` | 'contrast' or 'centered', The type of data scaling used for plotting. Either the fold change ('contrast') or the centered log2-intensity ('centered').
`plot` | Logical(1), If `TRUE` (default) the barplot is produced. Otherwise (if `FALSE`), the summaries which the barplot is based on are returned.

### Value

A barplot (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, normalize and impute missing values
    filt <- filter_missval(se, thr = 0)
    norm <- normalize_vsn(filt)
    imputed <- impute(norm, fun = "MinProb", q = 0.01)

    # Test for differentially expressed proteins
    diff <- test_diff(imputed, "control", "Ctrl")
    dep <- add_rejections(diff, alpha = 0.05, lfc = 1)

    # Plot single proteins
    plot_single(dep, 'USP15')
    plot_single(dep, 'USP15', 'centered')
    plot_single(dep, c('USP15', 'CUL1'))
    plot_single(dep, c('USP15', 'CUL1'), plot = FALSE)

[Package DEP version 1.2.0 Index]