Draws superposed density plots, one 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 density curves are colored by factor level to better
visualize the differences.
A SpC matrix with proteins in the rows and samples in the columns.
minSpC
All matrix cells with values below this threshold are excluded.
fact
NULL or a factor of length equal to the number of columns in the expression
matrix. If provided the density curves are colored by factor level.
...
Extra parameters passed to the plot function.
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.densityplots(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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'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
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> 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.densityplots.Rd_%03d_medium.png", width=480, height=480)
> ### Name: spc.densityplots
> ### Title: SpC density plots of a SpC matrix
> ### Aliases: spc.densityplots
> ### Keywords: plots
>
> ### ** Examples
>
> data(msms.dataset)
> spc.densityplots(exprs(msms.dataset),fact=pData(msms.dataset)[,1],
+ main="UPS1 200fm vs 600fm")
>
>
>
>
>
> dev.off()
null device
1
>