groupPlot: groupPlot

In mjhelf/Metaboseek: Metaboseek platform

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.