PlotIntensity {MQmetrics} | R Documentation |
Intensity / LFQ intensity per sample.
PlotIntensity( MQCombined, split_violin_intensity = TRUE, intensity_type = "Intensity", log_base = 2, long_names = FALSE, sep_names = NULL, palette = "Set2" )
MQCombined |
Object list containing all the files from the MaxQuant
output. It is the result from using |
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'. |
A violin plot and boxplot of the intensities in each sample.
MQPathCombined <- system.file("extdata/combined/", package = "MQmetrics") MQCombined <- make_MQCombined(MQPathCombined) PlotIntensity(MQCombined)