EICgeneral: EICgeneral

View source: R/Functions_plotting_EICs.R

EICgeneralR 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.

Value

sends a grouped EIC plot to the current plotting device, or generates a .pdf file


mjhelf/Mosaic documentation built on April 28, 2022, 11:32 a.m.