EICgeneral: EICgeneral
In mjhelf/Mosaic: Metaboseek platform

View source: R/Functions_plotting_EICs.R

EICgeneral

R Documentation

EICgeneral

Description

wrapper function to plot multiple EICs

Usage

EICgeneral(
  rtmid,
  mzmid,
  glist,
  cols = NULL,
  colrange = "Mseek.colors",
  transparency = 1,
  RTall = FALSE,
  TICall = FALSE,
  rtw = 30,
  ppm = 5,
  rdata,
  pdfFile = "plotOutput.pdf",
  leadingTIC = T,
  lw = 1,
  adducts = c(0),
  cx = 1,
  midline = T,
  yzoom = 1,
  RTcorrect = NULL,
  importEIC = NULL,
  globalYmax = FALSE,
  subtitles = NULL,
  raise = F,
  relPlot = F,
  margins = NULL,
  ylabshift = 0,
  RescaleExclude = NULL
)

Arguments

`rtmid`	vector of retention time values (not ranges). If length >1, multiple plots are called (multiple pages in pdf file)
`mzmid`	vector of mz values (not ranges). Has to be same length as `rtmid`
`glist`	a named list of grouped file names (as supplied in $grouping of rawLayout objects)
`cols`	integer, number of columns in plot. if NULL, grid can be defined externally
`colrange`	character(1), color range function used for line colors, OR a list of data.frames, see `Details`
`transparency`	numeric(1), alpha (range 0..1) for transparency of lines
`RTall`	if TRUE, entire RT range will be plotted
`TICall`	if TRUE, TIC will be plotted instead of EIC
`rtw`	retention time window +/- rtmid in seconds that will be plotted
`ppm`	mz window +/- mzmid in ppm that will be plotted
`rdata`	named list of xcmsRaw objects
`pdfFile`	character - if not NULL, plotting result will be saved in a pdf file with this name.
`leadingTIC`	if TRUE, a TIC plot is made before the EIC plots (e.g. as first page of pdf file)
`lw`	line width for plot lines
`adducts`	numeric() of mass shifts to be added to feature masses
`cx`	character expansion factor (font size)
`midline`	if TRUE, dotted vertical line should be plotted at feature rt
`yzoom`	zoom factor into y-axis
`RTcorrect`	if not NULL, this RTcorr object will be used to adjust retention times.
`importEIC`	a `multiEICplus()` output object to plot here, If NULL, `multiEICplus()` is called with the other supplied parameters
`globalYmax`	if TRUE, all EICs are scaled to the maximum value across all plotting groups instead of the maximum within each group
`subtitles`	subtitles for each EIC, must be character of same length as rtmid and mzmid or NULL
`raise`	if TRUE, EIC will be plotted with y axis going to -0.02*max(ylim) so that EICs with 0 intensity are visible.
`relPlot`	if TRUE, y-axis will show relative intensities
`margins`	manual setting for plot margins (par$mar)
`ylabshift`	shift horizontal position of y axis label
`RescaleExclude`	character(), exclude this group from rescaling, or NULL to use all

Details

colrange: A named list with the same structure as glist, but with a data.frame in each list element with row order corresponding to items in the list elements of glist and columns color and label, specifying the EIC color and legend label for each EIC trace.