string indicating the name of the column in the phenoData that
defines the groups
...
further arguments to be passed to the methods
Value
Object of class plot.mpm, i.e. the S3 output object of the plot.mpm
function of the mpm package
Note
Coloring of groups on the spectralMap uses the a4 palette as produced
by a4palette
Author(s)
Tobias Verbeke
References
Wouters, L., Goehlmann, H., Bijnens, L., Kass, S.U., Molenberghs, G.,
Lewi, P.J. (2003). Graphical exploration of gene expression data: a
comparative study of three multivariate methods. Biometrics59, 1131-1140.
Goehlmann, H. and W. Talloen (2009). Gene Expression Studies Using Affymetrix
Microarrays, Chapman & Hall/CRC, pp. 148 - 153.
See Also
spectralMap-methods, plot.mpm
Examples
if (require(ALL)){
data(ALL, package = "ALL")
ALL <- addGeneInfo(ALL)
spectralMap(object = ALL, groups = "BT", legendPos = 'bottomright')
spectralMap(object = ALL, groups = "BT",
plot.mpm.args = list(label.tol = 10, rot = c(-1, 1), sub = "", lab.size = 0.65,
dim = c(1,2), sampleNames = FALSE, zoom = c(1,5), col.size = 2,
do.smoothScatter = TRUE))
spectralMap(object = ALL, groups = "BT",
plot.mpm.args = list(label.tol = 10, rot = c(-1, 1), sub = "", lab.size = 0.65,
dim = c(1,2), sampleNames = as.character(pData(ALL)$BT),
zoom = c(1,5), col.size = 2, do.smoothScatter = TRUE))
}
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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Type 'license()' or 'licence()' for distribution details.
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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(a4Base)
Loading required package: grid
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")'.
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: annaffy
Loading required package: GO.db
Loading required package: KEGG.db
KEGG.db contains mappings based on older data because the original
resource was removed from the the public domain before the most
recent update was produced. This package should now be considered
deprecated and future versions of Bioconductor may not have it
available. Users who want more current data are encouraged to look
at the KEGGREST or reactome.db packages
Loading required package: mpm
Loading required package: MASS
Attaching package: 'MASS'
The following object is masked from 'package:AnnotationDbi':
select
Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
mpm version 1.0-22
Loading required package: genefilter
Attaching package: 'genefilter'
The following object is masked from 'package:MASS':
area
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Loading required package: multtest
Loading required package: glmnet
Loading required package: Matrix
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Loading required package: foreach
Loaded glmnet 2.0-5
Loading required package: a4Preproc
Loading required package: a4Core
Attaching package: 'a4Core'
The following object is masked from 'package:limma':
topTable
Loading required package: gplots
Attaching package: 'gplots'
The following object is masked from 'package:multtest':
wapply
The following object is masked from 'package:IRanges':
space
The following object is masked from 'package:S4Vectors':
space
The following object is masked from 'package:stats':
lowess
a4Base version 1.20.0
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/a4Base/spectralMap.Rd_%03d_medium.png", width=480, height=480)
> ### Name: spectralMap
> ### Title: Draw a Spectral Map
> ### Aliases: spectralMap
> ### Keywords: hplot
>
> ### ** Examples
>
> if (require(ALL)){
+ data(ALL, package = "ALL")
+ ALL <- addGeneInfo(ALL)
+
+ spectralMap(object = ALL, groups = "BT", legendPos = 'bottomright')
+
+ spectralMap(object = ALL, groups = "BT",
+ plot.mpm.args = list(label.tol = 10, rot = c(-1, 1), sub = "", lab.size = 0.65,
+ dim = c(1,2), sampleNames = FALSE, zoom = c(1,5), col.size = 2,
+ do.smoothScatter = TRUE))
+
+ spectralMap(object = ALL, groups = "BT",
+ plot.mpm.args = list(label.tol = 10, rot = c(-1, 1), sub = "", lab.size = 0.65,
+ dim = c(1,2), sampleNames = as.character(pData(ALL)$BT),
+ zoom = c(1,5), col.size = 2, do.smoothScatter = TRUE))
+ }
Loading required package: ALL
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db
>
>
>
>
>
> dev.off()
null device
1
>