plot_all {DEP} | R Documentation

## Visualize the results in different types of plots

### Description

`plot_all` visualizes the results of the differential protein expression analysis in different types of plots. These are (1) volcano plots, (2) heatmaps, (3) single protein plots, (4) frequency plots and/or (5) comparison plots.

### Usage

    plot_all(dep, plots = c("volcano", "heatmap", "single", "freq",
      "comparison"))

### Arguments

`dep` | SummarizedExperiment, Data object which has been generated by `analyze_dep` or the combination of `test_diff` and `add_rejections`.
`plots` | "volcano", "heatmap", "single", "freq" and/or "comparison",

### Value

Pdfs containg the desired plots.

### Examples

    # Load datasets
    data <- UbiLength
    exp_design <- UbiLength_ExpDesign

    # Import and process data
    se <- import_MaxQuant(data, exp_design)
    processed <- process(se)

    # Differential protein expression analysis
    dep <- analyze_dep(processed, "control", "Ctrl")

    ## Not run:
    # Plot all plots
    plot_all(dep)

    ## End(Not run)

[Package DEP version 1.12.0 Index]