plotIntDistr: Plot the distribution of the peaks intensity

In wenbostar/metaX: A flexible and comprehensive software for processing omics data.

Plot the distribution of the peaks intensity

Description

Plot the distribution of the peaks intensity for both raw intensity and normalized intensity.

Usage

plotIntDistr(x, width = 14, sortBy = "order", rmNA = TRUE,
  ylim = NULL, ...)

Arguments

x	A metaXpara object.
width	The width of pdf, default is 14.
sortBy	Sort the samples according to order (default), batch or class
rmNA	Whether or not to consider NA, default is TRUE. When this value is FALSE, NA will be considered as 0 then all values are +1.
...	Additional parameter

Value

The figure name

Author(s)

Bo Wen [e-mail]

Examples

library(faahKO)
xset <- group(faahko)
xset <- retcor(xset)
xset <- group(xset)
xset <- fillPeaks(xset)
peaksData <- as.data.frame(groupval(xset,"medret",value="into"))
peaksData$name <- row.names(peaksData)
para <- new("metaXpara")
rawPeaks(para) <- peaksData
sampleListFile(para) <- system.file("extdata/faahKO_sampleList.txt", 
    package = "metaX")
para <- reSetPeaksData(para)
plotIntDistr(para)
## after normalization
para <- metaX::normalize(para)
plotIntDistr(para)

wenbostar/metaX documentation built on July 4, 2023, 7:50 p.m.