analysisinfo-dataframe: AnalysisInfo data.frame methods
In rickhelmus/patRoon: Workflows for Mass-Spectrometry Based Non-Target Analysis

analysisinfo-dataframe

R Documentation

AnalysisInfo data.frame methods

Description

Various parsing and plotting functions for the analysisInfo data.frame.

Usage

## S4 method for signature 'data.frame'
getTICs(obj, retentionRange = NULL, MSLevel = 1)

## S4 method for signature 'data.frame'
getBPCs(obj, retentionRange = NULL, MSLevel = 1)

## S4 method for signature 'data.frame'
plotTICs(
  obj,
  retentionRange = NULL,
  MSLevel = 1,
  retMin = FALSE,
  title = NULL,
  colourBy = c("none", "analyses", "rGroups"),
  showLegend = TRUE,
  xlim = NULL,
  ylim = NULL,
  ...
)

## S4 method for signature 'data.frame'
plotBPCs(
  obj,
  retentionRange = NULL,
  MSLevel = 1,
  retMin = FALSE,
  title = NULL,
  colourBy = c("none", "analyses", "rGroups"),
  showLegend = TRUE,
  xlim = NULL,
  ylim = NULL,
  ...
)

Arguments

`obj`	An `analysisInfo` data.frame object as obtained by generateAnalysisInfo function.
`retentionRange`	Range of retention time (in seconds), m/z, respectively. Should be a numeric vector with length of two containing the min/max values. The maximum can be Inf to specify no maximum range. Set to NULL to skip this step.
`MSLevel`	Integer vector with the ms levels (i.e., 1 for MS1 and 2 for MS2) to obtain traces.
`retMin`	Plot retention time in minutes (instead of seconds).
`title`	Character string used for title of the plot. If `NULL` a title will be automatically generated.
`colourBy`	Sets the automatic colour selection: "none" for a single colour or "analyses"/"rGroups" for a distinct colour per analysis or analysis replicate group.
`showLegend`	Plot a legend if TRUE.
`xlim`, `ylim`	Sets the plot size limits used by `plot`. Set to `NULL` for automatic plot sizing.
`...`	Further arguments passed to `plot`.

Functions

getTICs(data.frame): Obtain the total ion chromatogram/s (TICs) of the analyses.
getBPCs(data.frame): Obtain the base peak chromatogram/s (BPCs) of the analyses.
plotTICs(data.frame): Plots the TICs of the analyses.
plotBPCs(data.frame): Plots the BPCs of the analyses.