Generate Concept-Gene Tabulates

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Description

A function to generate specified Concept-Gene Tabulates

Usage

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geneAnswersHeatmap(x, showCats = c(1:5), catTerm = FALSE, geneSymbol = FALSE, catID=FALSE, nameLength='all', showAllGenes=FALSE, ...)

Arguments

x

an instance of GeneAnswers objects

showCats

a numeric or string vector specified categories

catTerm

a logic value to specify whether mapping category IDs to category names

geneSymbol

a logic value to specify whether mapping gene IDs to gene symbols

catID

a logic value to specify whether show category IDs when catTerm is set to TRUE

nameLength

show how many first letters for long term names, 'all' for full name

showAllGenes

logic, show all genes in the heatmap or not

...

other parameters used by geneAnnotationHeatmap

Details

This function generates concept-gene tabulates for an input GeneAnswers instance. The concept-gene tabulates contain two maps. Left side is a heatmap based on given expression matrix. Right side is a concept-gene map, which could be represented as two-color heatmap or table.

Value

The function will generate a map without return value.

Author(s)

Gang Feng, Pan Du and Simon Lin

References

Feng, G., Du, P., Krett, N., Tessel, M., Rosen, S., Kibbe, W.A. and Lin, S.M., 'A collection of bioconductor methods to visualize gene-list annotations', BMC Research Notes 2010, 3:10

See Also

geneAnnotationHeatmap

Examples

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example(GeneAnswers)
## Not run: geneAnswersHeatmap(x, catTerm=TRUE, geneSymbol=TRUE)

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