PlotIntensity {MQmetrics} | R Documentation

## Intensity / LFQ intensity per sample.

### Description

Intensity / LFQ intensity per sample.

### Usage

    PlotIntensity(
      MQCombined,
      split_violin_intensity = TRUE,
      intensity_type = "Intensity",
      log_base = 2,
      long_names = FALSE,
      sep_names = NULL,
      palette = "Set2"
    )

### Arguments

`MQCombined` | Object list containing all the files from the MaxQuant output. It is the result from using `make_MQCombined`.
`split_violin_intensity` | If TRUE, both the LFQ and the Intensity will be shown in the same plot. If FALSE, it can be specified in the intensity_type which intensity to visualize.
`intensity_type` | The type of intensity. Values: 'Intensity' or 'LFQ'. Only useful if split_violin_intensity = FALSE. Default is Intensity.
`log_base` | The logarithmic scale for the intensity. Default is 2.
`long_names` | If TRUE, samples having long names will be considered, and the name will be split by sep_names. By default = FALSE.
`sep_names` | If long_names is TRUE, sep_names has to be selected. Samples names will be split. By default is NULL.
`palette` | The palette from the Package RColorBrewer. By default is 'Set2'.

### Value

A violin plot and boxplot of the intensities in each sample.

### Examples

    MQPathCombined <- system.file("extdata/combined/", package = "MQmetrics")
    MQCombined <- make_MQCombined(MQPathCombined)
    PlotIntensity(MQCombined)

[Package MQmetrics version 1.0.0 Index]