Heatmap representing signals in given ranges

Description

plot heatmap in the given feature ranges

Usage

featureAlignedHeatmap(cvglists, feature.gr, upstream, downstream, 
             zeroAt, n.tile=100, 
             annoMcols=c(), sortBy=names(cvglists)[1],
             color=colorRampPalette(c("yellow", "red"))(50),
             lower.extreme, upper.extreme,
             margin=c(0.1, 0.01, 0.15, 0.1), gap=0.01, 
             newpage=TRUE, gp=gpar(fontsize=10),
             ...)

Arguments

Value

invisible gList object.

Author(s)

Jianhong Ou

See Also

See Also as featureAlignedSignal, featureAlignedDistribution

Examples

  cvglists <- list(A=RleList(chr1=Rle(sample.int(5000, 100), 
                                      sample.int(300, 100))), 
                   B=RleList(chr1=Rle(sample.int(5000, 100), 
                                      sample.int(300, 100))))
  feature.gr <- GRanges("chr1", IRanges(seq(1, 4900, 100), width=100))
  feature.gr$anno <- rep(c("type1", "type2"), c(25, 24))
  featureAlignedHeatmap(cvglists, feature.gr, zeroAt=50, annoMcols="anno")

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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> library(ChIPpeakAnno)
Loading required package: grid
Loading required package: IRanges
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: 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: Biostrings
Loading required package: XVector
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: VennDiagram
Loading required package: futile.logger

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ChIPpeakAnno/featureAlignedHeatmap.Rd_%03d_medium.png", width=480, height=480)
> ### Name: featureAlignedHeatmap
> ### Title: Heatmap representing signals in given ranges
> ### Aliases: featureAlignedHeatmap
> ### Keywords: misc
> 
> ### ** Examples
> 
>   cvglists <- list(A=RleList(chr1=Rle(sample.int(5000, 100), 
+                                       sample.int(300, 100))), 
+                    B=RleList(chr1=Rle(sample.int(5000, 100), 
+                                       sample.int(300, 100))))
>   feature.gr <- GRanges("chr1", IRanges(seq(1, 4900, 100), width=100))
>   feature.gr$anno <- rep(c("type1", "type2"), c(25, 24))
>   featureAlignedHeatmap(cvglists, feature.gr, zeroAt=50, annoMcols="anno")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>