violinPlotImp: Comparative Violin Plot Constructor

In AurelieGuilbault/VIQCing: Data Processing For Metabolomic Data

Description

Construct Violin plots from imputed dataset and cleaned by QC.r. Produces a pdf File containing the plots.

Usage

violinPlotImp(input, inputImputed = paste0(strsplit(input, ".", fixed =
  TRUE)[[1]][1], "_imputed.txt"), output = paste0(strsplit(input, ".",
  fixed = TRUE)[[1]][1], "_Imputed.pdf"), na = F, numberByGraph = 1,
  colNumberByPage = 5, rowNumberByPage = 2, landscape = F,
  compound = NULL, metabolite = NULL, sampleStart = 3,
  compoundImp = NULL, metaboliteImp = NULL, sampleStartImp = 3,
  onlyImputed = TRUE)

Arguments

input	name of the cleaned datafile; Must contain: -a column named "Compound"; -a column named "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..
inputImputed	name of the imputed 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.
compoundImp	default NULL, position of the compound column for Imputed dataset if named otherwise;
metaboliteImp	default NULL, position of the metabolite column for Imputed dataset if named otherwise;
sampleStartImp	default 3, 1st column of the compounds intensity for Imputed dataset.
onlyImputed	default TRUE, TRUE will display only plots for metabolites with imputed values. (nb_imputed > 0)

Details

it is possible to put any 2 corresponding files, as long as they have the same row and column names. (The imputation part is not necessary, but it is the principal input type of this function. The legend and labels does contain the term "Imputed" by default.)

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 2 dataset with the following headers ; Compound, Metabolite, Sample #1, ...
violinPlotQC<- function("dummySet.txt")

for an imputed dataset with the following header ; compound, metabolite,  Sample #1, ...
violinPlotQC<- function("dummySet.txt", compoundImp = 1, metaboliteImp = 2)

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