RowOrderExtractor: Extract row order from a hclust object stored in a...
In ATpoint/misterplotR: Functions for plotting and clustering of count data

Description Usage Arguments Details Author(s) Examples

View source: R/src_RowOrderExtractor.R

This function (in a chronological order) comes right after running PlotHtmp. The function will take the returned output of PlotHtmp plus either a GRanges object or a list of gene of region names and will then extract the rows that belong to each cluster as defined in PlotHtmp.

RowOrderExtractor(
  HtmpObject,
  ReferenceData,
  Type,
  ToDisk = FALSE,
  OutputDir = "./",
  OutputName = "",
  WithDate = FALSE,
  RangedIs1Based = TRUE
)

`HtmpObject`	the output of `PlotHtmp`
`ReferenceData`	a GRanges object (when using ranged data) or a vector with names in the same order as used for `PlotHtmp` from which the rows will be extracted according clustering from `PlotHtmp`
`Type`	either "ranged" or "unranged", must be ranged when using GRanges input
`ToDisk`	whether to write the ranges or names of each cluster to disk
`OutputDir`	output directory for ToDisk
`OutputName`	name prefix for ToDisk
`WithDate`	logica, whether to prefix files written to disk with date
`RangedIs1Based`	Whether GRanges is 1-based so subtract 1 from start prior to writing to disk as BED

During PlotHtmp there is an option to split the rows into clusters according to hclust output. In order to get the elements per cluster one could use cutree but since we want to ensure that the output order of the elements is 100 the returned heatmap object.

Alexander Toenges

Gr <- GRanges(seqnames = rep("chr1", 2000), ranges = IRanges(start = seq(1,1000), end = rep(1001, 2000)))
cts <- sapply(seq(1,10), function(x) rnorm(1000,10))
rownames(cts) <- paste0("gene", seq(1,1000))
Htmp <- PlotHtmp(InputData = cts, Htmp.hclustRow = hclust(dist(cts)), Htmp.nclusters = 3, Htmp.return = TRUE)
Extracted.unranged <- RowOrderExtractor(HtmpObject = Htmp, ReferenceData = rownames(cts), Type = "unranged")
Extracted.ranged <- RowOrderExtractor(HtmpObject = Htmp, ReferenceData = Gr, Type = "ranged")