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

  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")