R: Create double-labeled MDS plot from (merged) ExpressionSet
plotMDS
R Documentation
Create double-labeled MDS plot from (merged) ExpressionSet
Description
Create Multidimensional Scaling (MDS) plot from ExpressionSet. Very similar to Principal Component Analysis (PCA) plots all samples are plotted in a two-dimensional space where both axis represent the two principle axis of expression variation. In this plot each sample can be labeled with a color and with a symbol.
colname in pData(eset) to retrieve information for the labeling of samples with a color. All samples with the same value in pData(eset)[,colLabel] will share the same color.
symLabel
colname in pData(eset) to retrieve information for the labeling of samples with a symbol. All samples with the same value in pData(eset)[,symLabel] will share the same symbol.
legend
If TRUE a legend will be provided next to the MDS plot for both colLabel and symlabel.
file
If defined, the resulting plot will be stored as a pdf file instead of shown interactively.
...
Additional parameters for the 'plot' function (e.g. 'main').
Examples
# retrieve two datasets:
library(inSilicoDb);
InSilicoLogin("rpackage_tester@insilicodb.com", "5c4d0b231e5cba4a0bc54783b385cc9a");
eset1 = getDataset("GSE18842", "GPL570", norm="FRMA", features="gene");
eset2 = getDataset("GSE31547", "GPL96", norm="FRMA", features="gene");
esets = list(eset1,eset2);
# merge them using no additional merging technique and the 'COMBAT' method:
library(inSilicoMerging)
eset_FRMA = merge(esets);
eset_COMBAT = merge(esets, method="COMBAT");
# check available annotations:
colnames(pData(eset_FRMA))
table(pData(eset_FRMA)[,"Disease"]);
table(pData(eset_FRMA)[,"Study"]);
# Visual inspection of the two merged datasets through an MDS plot
plotMDS(eset_FRMA, colLabel="Disease", symLabel="Study")
plotMDS(eset_COMBAT, colLabel="Disease", symLabel="Study")
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.
> library(inSilicoMerging)
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")'.
Attaching package: 'inSilicoMerging'
The following object is masked from 'package:base':
merge
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/inSilicoMerging/plotMDS.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotMDS
> ### Title: Create double-labeled MDS plot from (merged) ExpressionSet
> ### Aliases: plotMDS
>
> ### ** Examples
>
>
> # retrieve two datasets:
> library(inSilicoDb);
Loading required package: rjson
Loading required package: RCurl
Loading required package: bitops
> InSilicoLogin("rpackage_tester@insilicodb.com", "5c4d0b231e5cba4a0bc54783b385cc9a");
INSILICODB: Welcome RPackage Tester
[1] 5296
> eset1 = getDataset("GSE18842", "GPL570", norm="FRMA", features="gene");
INSILICODB: The dataset you requested could not be computed. We are sorry for the inconvenience.
Error: Stopped because of previous errors
Execution halted
providing 
.