IBSpectra plots

Description

Various plots are implement to assure data quality, and accompany preprocessing and analysis.

reporterMassPrecision

reporterMassPrecision(x):

Calculates and displays the deviation from the 'true' tag mass - as specified in the IBSpectra object - of each channel.

reporterIntensityPlot

reporterIntensityPlot(x):

Displays boxplots of intensity of channels before and after normalization - useful to check the result of normalization.

raplot

raplot(x,...):

Ratio-Absolute intensity plot - will be deprecated by maplot

x

IBSpectra object

...

Parameters to plot function.

plotRatio

plotRatio(x,channel1,channel2,protein,...):

Plots abundances of one protein

x

IBSpectra object

channel1

channel2

protein

...

Parameters to plot function.

maplot

maplot(x,channel1,channel2,...):

Creates a ratio-versus-intensity plot.

x

IBSpectra object.

maplot2

maplot2():

Author(s)

Florian P. Breitwieser, Jacques Colinge

See Also

IBSpectra, isobar-preprocessing isobar-analysis

Examples

data(ibspiked_set1)
maplot(ibspiked_set1,main="IBSpiked, not normalized")
maplot(normalize(ibspiked_set1),main="IBSpiked, normalized")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(isobar)
Loading required package: Biobase
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

Welcome to Bioconductor

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

Welcome to isobar (v 1.18.0)
   'openVignette("isobar")' and '?isobar' provide help on usage.


Attaching package: 'isobar'

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

    normalize

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

    paste0

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/isobar/isobar-plots.Rd_%03d_medium.png", width=480, height=480)
> ### Name: isobar-plots
> ### Title: IBSpectra plots
> ### Aliases: isobar-plots reporterMassPrecision
> ###   reporterMassPrecision,IBSpectra,missing-method
> ###   reporterMassPrecision,IBSpectra,logical-method reporterIntensityPlot
> ###   reporterIntensityPlot-methods reporterIntensityPlot,IBSpectra-method
> ###   raplot raplot,IBSpectra-method plotRatio
> ###   plotRatio,IBSpectra,character,character,character-method maplot
> ###   maplot,IBSpectra,missing,missing-method
> ###   maplot,IBSpectra,character,character-method
> ###   maplot,missing,numeric,numeric-method maplot2
> ###   maplot2,ANY,character,character-method
> ###   maplot2,list,character,character-method protGgdata
> ###   protGgdata,ANY,character,character-method
> 
> ### ** Examples
> 
> data(ibspiked_set1)
> maplot(ibspiked_set1,main="IBSpiked, not normalized")
> maplot(normalize(ibspiked_set1),main="IBSpiked, normalized")
LOG: is.normalized: TRUE
	normalizing ibspiked_set1.ibspectra.csv [14991 spectra]
LOG: normalization.multiplicative.factor file ibspiked_set1.ibspectra.csv channel 114: 0.8177
LOG: normalization.multiplicative.factor file ibspiked_set1.ibspectra.csv channel 115: 0.9634
LOG: normalization.multiplicative.factor file ibspiked_set1.ibspectra.csv channel 116: 1
LOG: normalization.multiplicative.factor file ibspiked_set1.ibspectra.csv channel 117: 0.9961
Warning message:
In normalize(ibspiked_set1) :
  Isotope impurity correction has not been logged - data might be uncorrected. See ?correctIsotopeImpurities.
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>