Set of SpC boxplots by sample

Description

Draws a boxplot for each column (sample) in a SpC matrix. The SpC are previosly transformed by log2, with an offset of 0.1. If a factor is provided the boxplots are colored by factor level to better visualize the differences.

Usage

spc.boxplots(msms.counts,fact=NULL,minSpC=2,...)

Arguments

Details

More informative plots are obtained when excluding the cells with values below 2, the default for minSpC.

Author(s)

Josep Gregori

Examples

data(msms.dataset)
spc.boxplots(exprs(msms.dataset),fact=pData(msms.dataset)[,1],
      main="UPS1 200fm vs 600fm")

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)

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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(msmsEDA)
Loading required package: 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/msmsEDA/spc.boxplots.Rd_%03d_medium.png", width=480, height=480)
> ### Name: spc.boxplots
> ### Title: Set of SpC boxplots by sample
> ### Aliases: spc.boxplots
> ### Keywords: plots
> 
> ### ** Examples
> 
> data(msms.dataset)
> spc.boxplots(exprs(msms.dataset),fact=pData(msms.dataset)[,1],
+       main="UPS1 200fm vs 600fm")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>