violinPlotQC: Simple Violin Plot Constructor

In AurelieGuilbault/VIQCing: Data Processing For Metabolomic Data

Description

Construct Violin plots for a metabolomic dataset cleaned by QC.r (not required). Produces a pdf File containing the plots.

Usage

violinPlotQC(input, output = paste0(strsplit(input, ".", fixed =
  TRUE)[[1]][1], ".pdf"), na = F, numberByGraph = 1,
  colNumberByPage = 5, rowNumberByPage = 2, landscape = F,
  compound = NULL, metabolite = NULL, sampleStart = 3)

Arguments

input	name of the cleaned datafile; Must contain: a column "Compound"; a column "Metabolite"; and all the columns sample from <sampleStart> to the end of the file; the rest doesn't matter and the names are optional, as long as the column position is entered.
output	default <input>.pdf, name of the final pdf file;
na	default FALSE, FALSE removes the untargeted (NA) metabolite from the plots;
numberByGraph	default 1, number of metabolite violin plots by graph window;
colNumberByPage	default 5, number of column in the output pdf file;
rowNumberByPage	default 2, number of row in the output pdf file;
landscape	default FALSE, orientation of the pdf file;
compound	default NULL, position of the compound column if named otherwise;
metabolite	default NULL, position of the metabolite column if named otherwise;
sampleStart	default 3, 1st column of the compounds intensity.

Details

Can be used on any kind of file containing rows with x (gene, metabolite, etc.) and column with y (Sample, patients, etc.).

Value

None

See Also

• ggplot2 packagehttps://www.rdocumentation.org/packages/ggplot2

• tidyr package https://www.rdocumentation.org/packages/tidyr

• gridExtra package https://www.rdocumentation.org/packages/gridExtra

• ggpubr package https://www.rdocumentation.org/packages/ggpubr

• scales package https://www.rdocumentation.org/packages/scales

Examples

for a dataset with the following header ; Compound, m/z, Metabolite, RT, Sample #1, ...
violinPlotQC<- function("dummySet.txt", sampleStart = 5)

for a dataset with the following header ; compound, m/z, metabolite, RT, Sample #1, ...
violinPlotQC<- function("dummySet.txt", compound = 1, metabolite = 3, sampleStart = 5)

AurelieGuilbault/VIQCing documentation built on Oct. 30, 2019, 5:02 a.m.