plotEnrichMap: Plot and save an enrichment map for results of GSEA or...

Description Usage Arguments Details Author(s) See Also Examples

Description

This is a generic function.

When implemented as the S4 method for objects of class GSCA, this function will plot and save an enrichment map for GSEA or Hypergeometric test results.

To use this function for objects of class GSCA:

plotEnrichMap(object, resultName="GSEA.results", gscs, ntop=NULL, allSig=TRUE, gsNameType="id", displayEdgeLabel=TRUE, layout= "layout.fruchterman.reingold", filepath=".", filename="test.png", output="png", ...)

Usage

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plotEnrichMap(object, ...)

Arguments

object

an object. When this function is implemented as the S4 method of class GSCA, this argument is an object of class GSCA.

...

other arguments. (see below for the arguments supported by the method of class GSCA)

resultName:

a single character value: 'HyperGeo.results' or 'GSEA.results'

gscs:

a character vector specifying the names of gene set collections of which the top significant gene sets will be plotted

ntop:

a single integer or numeric value indicating how many gene sets of top significance will be plotted.

allSig:

a single logical value. If 'TRUE', all significant gene sets (adjusted p-value < 'pValueCutoff' of slot 'para') will be used; otherwise, only top 'ntop' gene sets will be used.

gsNameType:

a single character value specifying the type of the gene set names that will be displayed as the names of nodes in the enrichment map. The type of the gene set names should be one of the following: "id", "term" or "none".

displayEdgeLabel:

a single logical value specifying whether or not to display the labels of the edges in the enrichment map

layout:

a single character value specifying the layout of the enrichment map. (see help(layout) of the package igraph)

filepath:

a single character value specifying where to store the enrichment map.

output:

a single character value specifying the format of output image: "pdf" or "png"

...

other arguments used by the function png or pdf such as 'width' and 'height'

Details

See help(viewEnrichMap) for more details about the enrichment map for GSEA.

Author(s)

Xin Wang [email protected]

See Also

viewEnrichMap

Examples

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## Not run: 
library(org.Dm.eg.db)
library(KEGG.db)
##load data for enrichment analyses
data("KcViab_GSCA")
##plot and save the enrichment map
plotEnrichMap(KcViab_GSCA, gscs=c("GO_MF"), allSig=TRUE, ntop=NULL, gsNameType="id", 
displayEdgeLabel=FALSE,layout="layout.fruchterman.reingold", filepath="~", 
filename="GO_MF.pdf",output="pdf", width=8, height=8)

## End(Not run)

HTSanalyzeR documentation built on May 2, 2018, 4:30 a.m.