groupPlot: groupPlot

View source: R/Functions_plotting_EICs.R

groupPlotR Documentation

groupPlot

Description

generate multiple EICs on one page

Usage

groupPlot(
  EIClist,
  grouping,
  plotProps = list(TIC = TRUE, cx = 1, colr = topo.colors(nrow(EIClist[[1]]), alpha =
    1), ylim = NULL, xlim = NULL, lw = 1, midline = 100, yzoom = 1),
  compProps = list(mfrow = c(1, 2), oma = c(0, 2, 8, 0), xpd = NA, bg = NA, header =
    paste0(names(EIClist)), header2 = NULL, pdfFile = NULL, pdfHi = 6, pdfWi = 12, cx =
    1, adductLabs = c("0", "1", "2")),
  raise = F,
  relPlot = F,
  margins = NULL,
  ylabshift = 0,
  RescaleExclude = NULL
)

Arguments

EIClist

list of EICs from multiEIC() or multiEICplus()

grouping

a named list of grouped file names (as supplied in $grouping of rawLayout objects)

plotProps

a list of settings for the individual plots, see Details

compProps

layoout options for the composite plot, see Details

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

plotProps

A list with these elements:

  • TIC if TRUE, TIC instead of EIC

  • cx numeric(1) font size (character expansion) factor

  • colr color range (actual vector of color values)

  • ylim data.frame or matrix of nrow = number of plotted features, with min and max visible rt value (in seconds) for each feature

  • xlim data.frame or matrix of nrow = number of plotted features, with min and max visible intensity value for each feature

  • midline numeric() of y-axis positions where a dotted vertical line should be plotted

  • lw line width for plot lines

  • yzoom zoom factor into y-axis

compProps
  • mfrow integer(2) rows and columns for plotting (cf. par(), mfrow)

  • oma numeric(4) outer margins (cf. par(), oma)

  • xpd drawing outside of plot region, cf. par(), xpd

  • bg background color, cf. par(), bg

  • header First (title) line of composite plot

  • header2 Subtitle line of composite plot

  • pdfFile character - if not NULL, plotting result will be saved in a pdf file with this name.

  • pdfHi pdf height in inches

  • pdfWi pdf width in inches

  • cx numeric(1) font size (character expansion) factor

  • adductLabs adduct labels (nonfunctional)

Value

sends a grouped EIC plot to the current plotting device


mjhelf/Metaboseek documentation built on April 23, 2022, 12:09 p.m.