ChIPpeakAnno (version 3.6.5)

featureAlignedHeatmap: 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

cvglists
Output of featureAlignedSignal or a list of SimpleRleList or RleList
feature.gr
An object of GRanges with identical width. If the width equal to 1, you can use upstream and downstream to set the range for plot. If the width not equal to 1, you can use zeroAt to set the zero point of the heatmap.
upstream, downstream
upstream or dwonstream from the feature.gr. It must keep same as featureAlignedSignal. It is used for x-axis label.
zeroAt
zero point position of feature.gr
n.tile
The number of tiles to generate for each element of feature.gr, default is 100
annoMcols
The columns of metadata of feature.gr that specifies the annotations shown of the right side of the heatmap.
sortBy
Sort the feature.gr by columns by annoMcols and then the signals of the given samples. Default is the first sample. Set to NULL to disable sort.
color
vector of colors used in heatmap
lower.extreme, upper.extreme
The lower and upper boundary value of each samples
margin
Margin for of the plot region.
gap
Gap between each heatmap columns.
newpage
Call grid.newpage or not. Default, TRUE
gp
A gpar object can be used for text.
...
Not used.

Value

invisible gList object.

See Also

See Also as featureAlignedSignal, featureAlignedDistribution

Examples

Run this code
  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")

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