PlotIntensity: Intensity / LFQ intensity per sample.

In BioAlvaro/ProteoMS: Quality Control of Protemics Data

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)

BioAlvaro/ProteoMS documentation built on Jan. 12, 2022, 9:46 a.m.