Plots a chromatogram

Description

The method plot the chromatogram for various types in inputs (see below). Additional arguments are

y

One of "tic" (default) or "bpi" to plot the total ion current of base peak intensity chromatogram.

f

Optional and only when the input is a data.frame. Otherwise, it is extracted automatically from object. f is used to print the filename on the figure.

legend

A logical defining if the figure should be annotated.

plot

A logical defining if the plot should be rendered.

ms

A numeric defining what MS level spectra to use. Default is 1L.

...

Additional arguments passed to the plot function.

xcms::plotChrom provides a similar functionality.

Value

The methods invisibly return the data.frame with the retention times (rt column) and intensities (either tic or bpi) used to generate the figure.

Methods

signature(object = "character")

Plots the chromatogram for the mass-spectrometry data stored in the object file. The file format must be support by mzR. See mzR::openMSfile for details.

signature(object = "mzRramp")

Plots the chromatogram for the mzRramp instance. See the mzR package for details.

signature(object = "data.frame")

Plots the chromatogram using the relevant columns from the data.frame instance, i.e retentionTime and totIonCurrent (for tic) and basePeakIntensity (for bpi). Such a data.frame would typically be generated by extracting the header from an mzRramp instance. See mzR::header for details.

Examples

f <- system.file("lockmass/LockMass_test.mzXML", package = "msdata")
x <- chromatogram(f, main = "Source: mzXML file")
head(x)
dim(x)
x <- chromatogram(f, main = "Source: mzXML file",
                  ylim = c(0, 100))
## Not run: 
    library("mzR")
    ms <- openMSfile(f)
    chromatogram(ms, main = "Source: mzRramp",
                 col = "red")
    hd <- header(ms)
    chromatogram(hd, main = "Source: mzRramp header",
                 lty = "dashed")

    library("RforProteomics")
    f <- getPXD000001mzXML()
    chromatogram(f)
    grid()
  
## End(Not run)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(MSnbase)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics

This is MSnbase version 1.20.7 
  Read '?MSnbase' and references therein for information
  about the package and how to get started.


Attaching package: 'MSnbase'

The following object is masked from 'package:stats':

    smooth

The following object is masked from 'package:base':

    trimws

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MSnbase/chromatogram-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: chromatogram-methods
> ### Title: Plots a chromatogram
> ### Aliases: chromatogram-methods chromatogram,data.frame-method
> ###   chromatogram,character-method chromatogram,mzRramp-method
> ###   chromatogram
> ### Keywords: methods
> 
> ### ** Examples
> 
> f <- system.file("lockmass/LockMass_test.mzXML", package = "msdata")
> x <- chromatogram(f, main = "Source: mzXML file")
> head(x)
     rt      tic
1 0.300 97.70424
2 0.568 27.70334
3 0.784 27.34622
4 1.001 27.57260
5 1.217 26.60848
6 1.434 26.51795
> dim(x)
[1] 400   2
> x <- chromatogram(f, main = "Source: mzXML file",
+                   ylim = c(0, 100))
> ## Not run: 
> ##D     library("mzR")
> ##D     ms <- openMSfile(f)
> ##D     chromatogram(ms, main = "Source: mzRramp",
> ##D                  col = "red")
> ##D     hd <- header(ms)
> ##D     chromatogram(hd, main = "Source: mzRramp header",
> ##D                  lty = "dashed")
> ##D 
> ##D     library("RforProteomics")
> ##D     f <- getPXD000001mzXML()
> ##D     chromatogram(f)
> ##D     grid()
> ##D   
> ## End(Not run)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>