Concept-Gene Networking Plotting

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Description

A function to generate a concept-gene network by given gene information

Usage

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geneAnswersConcepts(x, centroidSize=c('geneNum', 'pvalue', 'foldChange', 'oddsRatio', 'correctedPvalue'), output=c('fixed','interactive'), showCats=c(1:5), catTerm=FALSE, catID=FALSE)

Arguments

x

a GeneAnswers instance.

centroidSize

type to represent the size of concepts.

output

output type of final output.

showCats

a numeric or string vector specified categories

catTerm

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

catID

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

Details

centroidSize could be one of "geneNum", "pvalue", "foldChange", "oddsRatio", "correctedPvalue". Each one defines to which the size of cencept dot is proportional geneNum: number of genes connecting to the concept pvalue: p value of enrichment test foldChange: fold of gene overrepresent in concepts oddsRatio: odds ratio of enrichment test correctedPvalue: adjusted p value of enrichment test output defines whether the final figure is interactive or not. Interactive figure calls igraph package to generate a tck/tk canvas. Fixed figure is a non-interactive png figure.

Value

One category-linkage figure is generated. It could be a R figure or tcltk figure depends on how the user set parameter output.

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

categoryNet

Examples

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example(GeneAnswers)
## Not run: geneAnswersConcepts(x, centroidSize='pvalue', output='interactive')

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