plotFlowgrams-proFIAset-method: Plot raw temporal profiles of the selected group.

In adelabriere/proFIA: Preprocessing of FIA-HRMS data

Description

Plot raw temporal profiles from proFIAset object corresponding to one or more molecules. The function will priorize index, only using mz if index is set to NULL. As this require to come back to the raw data, this can take some times, an we don't recommend using it on more than 30 files. It is better to choose 30 files in the proFIAset object.

Usage

## S4 method for signature 'proFIAset'
plotFlowgrams(object, index = NULL, mz = NULL,
  subsample = NULL, ppm = 5, margin = 2e-04, posleg = c("topright",
  "bottomright", "bottom", "bottomleft", "left", "topleft", "top", "right",
  "center"), title = NULL, scaled = FALSE, area = FALSE, ...)

Arguments

object	A proFIAset object.
index	The index of the group to be plotted.
mz	An mz value to be looked for only used if index is null. the research use the findMzGroup function.
subsample	A subset of sample to be plotted.
ppm	The tolerance for the research if mz is provided.
margin	An area outer the EICs mz range on which the EIC may be extended.
posleg	The position of the legend on the figure. See legend.
title	An optional vector of title for the plot. Need to be of the same
scaled	Shall all the EIC be put on the same scale with maximum to 1.
area	Shall the detectged area be plotted using transparency.
...	Supplementary graphical parameters to be passed to lines. length than index.

Value

No returned value

Examples

if(require(plasFIA)){
    data(plasMols)
    data(plasSet)
    plotFlowgrams(plasSet,mz=plasMols[7,"mass_M+H"])
}

adelabriere/proFIA documentation built on July 12, 2019, 5:46 a.m.