draw_TICspectrum: Draw TIC spectrum

Description Usage Arguments Value Examples

View source: R/draw_TICspectrum.R

Description

Based on the measures preprocessed by the function precook_measures(), the function draw_TICspectrum() pretends to draw the TIC spectrum of diferent samples

Usage

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draw_TICspectrum(cdf_folder, samplestodraw_TIC = NA,
  samplestodraw_altTIC = NA, samplestodraw_LOGTIC = NA,
  samplestodraw_LOGaltTIC = NA, colors = NULL)

Arguments

cdf_folder

directory containing the precooked measures (files preckd_measures.rda and preckd_variables.rda). Presumabily should be the same directory where the original measures are (ncdf4 files). E.g. cdf_folder="C:/esborrar_mesuresGcxGc/mesures_Berkely_Noelia"

samplestodraw_TIC

list of samples whose TIC spectrum needs to be drawed. The samples shoul be referred by their file position on a alphabetical ordered file list. Moreover, it can be drawed the result of adding or substracting a combination of samples; that operation should be indicated with a vector of samples, indicating with a minus the sample that should be substracted. e.g. list(1,2,c(1,-3)) means draw the 1st and second sample, as well as the result of substract the 3rd sample from the 1st

samplestodraw_altTIC

analogously to the previous argument, list of samples whose "altered" TIC spectrum needs to be drawed. Altered TIC is refered to a TIC without specific masses (see precook_measures() function). See the samplestodraw_TIC argument for further details.

samplestodraw_LOGTIC

list of samples whose log(TIC) spectrum needs to be drawed. e.g. samplestodraw_LOGTIC=list(c(1,-3),2) draws two plots, log(TIC(sample3)-log(TIC(sample1) and log(TIC(sample2).

samplestodraw_LOGaltTIC

analogously to the samplestodraw_LOGTIC argument, list of samples whose TIC spectrum needs to be drawed logarithmically. The only diference is that the TIC ploted is the altered one, a TIC without specific masses (see precook_measures() function).

colors

Colors used to draw the diferent spectrum samples. Visit http://colorbrewer2.org to improve your ideas. e.g. colors=c("red","black","#fdc086","grey","#7fc97f")

Value

Different spectrums are drawn in the viewer tab. Moreover the parameters used for preprocessing the data (through precook_measures()) are printed on screen as remembrance.

Examples

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draw_TICspectrum(cdf_folder="C:/esborrar_mesuresGcxGc/mesures_Berkely_Noelia", samplestodraw_altTIC = list(1), samplestodraw_LOGTIC = list(c(2,-3),2,3), colors=c("red","black","orange","green"))

jmbadia/GcxGctools documentation built on May 19, 2019, 4:06 p.m.