plot Tracks with additional DataTrack information added to the left of the plot

Description

plot Tracks with additional DataTrack information added to the left of the plot

Usage

plotTracksWithDataTrackInfo(trackList, labels = NULL, grange2show = NULL, dataTrackName = NULL, dataInfo = NULL, dataColorMap = NULL,
	dataInfoRange = NULL, dataBackground = gray(0.9), minHeatmapColumnWidth = 2, labelWidth = 0.1, 
	gradient = c("blue", "white", "red"), ncolor = 16, main = "", newPlot = FALSE, sizes = NULL, ...)

Arguments

Details

This function is adapted based on the plotTracks function in Gviz package. It adds sample labels to the heatmap dataTracks.

Value

Grid viewport layout information

Author(s)

Pan Du

See Also

See Also plotTracks, heatmapByChromosome

Examples

	data(exampleMethyGenoSet)
	if (require(TxDb.Hsapiens.UCSC.hg19.knownGene) && require(Gviz)) {
		## define data track
		exampleMethyGenoSet <- checkChrName(exampleMethyGenoSet)
		dTrack <- DataTrack(range=suppressWarnings(as(rowRanges(exampleMethyGenoSet), 'GRanges')), data=t(exprs(exampleMethyGenoSet)), 
			chromosome='chr21', type='heatmap')		

		## build annotation tracks
		annotationTracks <- buildAnnotationTracks('1826', includeGeneBody = FALSE, genomicFeature = "TxDb.Hsapiens.UCSC.hg19.knownGene", cytobandInfo=NA, CpGInfo=NA)
		trackList <- c(annotationTracks, list(dTrack))
		plotTracksWithDataTrackInfo(trackList, labels=colnames(exampleMethyGenoSet), grange2show = attr(annotationTracks, 'grange2show'))
	}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(methyAnalysis)
Loading required package: grid
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

Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
No methods found in "GenomicRanges" for requests: overlapsAny
No methods found in "genoset" for requests: rowRanges, rowRanges<-, toGenomeOrder
Warning messages:
1: multiple methods tables found for 'colMeans' 
2: multiple methods tables found for 'colSums' 
3: multiple methods tables found for 'rowMeans' 
4: multiple methods tables found for 'rowSums' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/methyAnalysis/plotTracksWithDataTrackInfo.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotTracksWithDataTrackInfo
> ### Title: plot Tracks with additional DataTrack information added to the
> ###   left of the plot
> ### Aliases: plotTracksWithDataTrackInfo
> ### Keywords: methods hplot
> 
> ### ** Examples
> 
> 
> 	data(exampleMethyGenoSet)
> 	if (require(TxDb.Hsapiens.UCSC.hg19.knownGene) && require(Gviz)) {
+ 		## define data track
+ 		exampleMethyGenoSet <- checkChrName(exampleMethyGenoSet)
+ 		dTrack <- DataTrack(range=suppressWarnings(as(rowRanges(exampleMethyGenoSet), 'GRanges')), data=t(exprs(exampleMethyGenoSet)), 
+ 			chromosome='chr21', type='heatmap')		
+ 
+ 		## build annotation tracks
+ 		annotationTracks <- buildAnnotationTracks('1826', includeGeneBody = FALSE, genomicFeature = "TxDb.Hsapiens.UCSC.hg19.knownGene", cytobandInfo=NA, CpGInfo=NA)
+ 		trackList <- c(annotationTracks, list(dTrack))
+ 		plotTracksWithDataTrackInfo(trackList, labels=colnames(exampleMethyGenoSet), grange2show = attr(annotationTracks, 'grange2show'))
+ 	}
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Loading required package: GenomicFeatures
Loading required package: Gviz
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>