R: Create gene-wise boxplot from (merged) ExpressionSet
plotGeneWiseBoxPlot
R Documentation
Create gene-wise boxplot from (merged) ExpressionSet
Description
Gene-wise boxplots describe the gene-wise distribution of samples. Sample can be grouped together using the batchLabel parameter and can be coloroed usig the colLabel parameter for optimal visualization of the possible batch effects.
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.
batchLabel
colname in pData(eset) to retrieve information for the grouping of samples. All samples with the same value in pData(eset)[,batchLabel] and with the same color will be grouped together.
gene
Gene for which the boxplot will be created. If not specified a random gene will be selected.
legend
If TRUE a legend will be provided next to the gene-wise box plot.
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 a random gene in the two merged datasets
gene = sample(rownames(exprs(eset_FRMA)), 1)
plotGeneWiseBoxPlot(eset_FRMA, colLabel="Disease", batchLabel="Study", gene=gene)
plotGeneWiseBoxPlot(eset_COMBAT, colLabel="Disease", batchLabel="Study", gene=gene)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> 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/plotGeneWiseBoxPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotGeneWiseBoxPlot
> ### Title: Create gene-wise boxplot from (merged) ExpressionSet
> ### Aliases: plotGeneWiseBoxPlot
>
> ### ** 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 
.