plotGeneWiseBoxPlot: Create gene-wise boxplot from (merged) ExpressionSet

Description Usage Arguments Examples

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.

Usage

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plotGeneWiseBoxPlot(eset, colLabel, batchLabel, gene=NULL, legend=TRUE, file=NULL, ...)

Arguments

eset

ExpressionSet object.

colLabel

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

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# retrieve two datasets:
library(inSilicoDb);
InSilicoLogin("[email protected]", "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)

inSilicoMerging documentation built on Oct. 5, 2016, 4:16 a.m.