sbcmsPlot: Plot the output from signal batch correction for the selected...

In computational-metabolomics/sbcms: Signal batch correction for (LC)-MS data

Description

Plot the output from signal batch correction for the selected or the first 100 features

Usage

sbcmsPlot(df, corrected_df, classes, batch, indexes = NULL,
  qc_label = "QC", output = "sbcms_plots.pdf")

Arguments

df	A data frame containing the original data before correction (samples in columns, features in rows).
corrected_df	A data frame containing the corrected data, as output by QCRSC
classes	A factor or character vector of sample classes. All QC samples should be labelled 'QC'.
batch	A vector indicating the batch each sample was measured in. If only one batch was measured then all values should be set to 1
indexes	Numeric vector defining whihc features from data frame to plot. If set to NULL will plot the first 100.
qc_label	Class label for QC sample.
output	Filename of the output pdf file. Can include the path. If set to NULL output will be list object containing ggplot2 plots.

Value

Pdf file or list object showing data before and after signal correction

Examples

classes <- sbcdata$class
batch <- sbcdata$batch
data <- t(sbcdata$data[, 1:20])
order <- c(1:ncol(data))
out <- QCRSC(d =data, order=order, batch=batch, classes=classes,
    spar=0, minQC=4)
plots <- sbcmsPlot (df=data, corrected_df=out, classes, batch,
    output=NULL) 

computational-metabolomics/sbcms documentation built on June 17, 2021, 12:22 a.m.