featureAlignedHeatmap: Heatmap representing signals in given ranges

In ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome 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.

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")

ChIPpeakAnno documentation built on April 1, 2021, 6:01 p.m.