Draws bars of height proportional to the sample size of each column
in a SpC matrix. The sizes are scaled to the median of the total SpC by sample.
Usage
spc.barplots(msms.counts,fact=NULL,...)
Arguments
msms.counts
A SpC matrix with proteins in the rows and samples in the columns.
fact
NULL or a factor of length equal to the number of columns in the expression
matrix. If provided the bars are colored by factor level.
...
Extra parameters passed to the plot function.
Details
.
Author(s)
Josep Gregori
Examples
data(msms.dataset)
spc.barplots(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)
R is free software and comes with ABSOLUTELY NO WARRANTY.
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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(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.barplots.Rd_%03d_medium.png", width=480, height=480)
> ### Name: spc.barplots
> ### Title: Set of SpC barplots by sample
> ### Aliases: spc.barplots
> ### Keywords: plots
>
> ### ** Examples
>
> data(msms.dataset)
> spc.barplots(exprs(msms.dataset),fact=pData(msms.dataset)[,1],
+ main="UPS1 200fm vs 600fm")
>
>
>
>
>
> dev.off()
null device
1
>