plotSegmentationHeatmap: Plot a heatmap diagram for a region along a chromosome

In tilingArray: Transcript mapping with high-density oligonucleotide tiling arrays

Description

Plot a heatmap diagram for a region along a chromosome

Usage

plotSegmentationHeatmap(dat, xlim, ylab, rowNames, 
                        chr=1, strand="+", vpr, colors, 		
                        colHeatmap=colorRamp(brewer.pal(9, "YlGnBu")), 
                        showConfidenceIntervals=TRUE,
                        just=c("left","centre"),
                        main,makeRasterImage = TRUE, ...)

Arguments

dat	list containing data to be plotted (see Details section below for particulars).
xlim	integer vector of length 2 with start and end coordinates (in bases) for plotting.
ylab	character scalar specifying y-axis label.
rowNames	character vector specifying a name for each row in the heatmap plot.
chr	integer of length 1 indicating the chromosome to plot (defaults to 1).
strand	character scalar which should be set to either + or - to indicate which strand of DNA to plot the intensity values from (defaults to "+").
vpr	which viewport to plot the figure in. If this function is called directly by the user this argument should be left missing.
colors	named character vector, optional. If missing, a default color scheme is used: c("+"="#00441b", "-"="#081d58", "duplicated"="grey", "cp"="#101010", "highlight"="red", "threshold"="grey"), where the first three elements refer to colors of data points and the last three to those of lines in the plot.
colHeatmap	function describing color scheme for the heatmap plot (defaults to YlGnBu from RColorBrewer package).
showConfidenceIntervals	logical scalar indicating whether confidence intervals for each change-point are to be plotted (only available once segmentation has occurred).
just	character vector specifying the justification of the supplied values to the given coordinates; setting the first entry to "left" indicates that the supplied x-coordinates are the start positions of the probes, change this to "centre" if the x-coordinates are the probe middle positions. Usually the second entry should be "centre" (see grid.rect)
main	character vector specifying plot title.
makeRasterImage	logical scalar indicating whether to plot the heatmap image by the grid.raster (see grid.raster) or the grid.rect (see grid.rect) function in grid package.The default is to generate raster image, as it can be displayed much faster with a relatively smaller file size.
...	additional arguments.

Details

This function is called by plotAlongChrom if the argument what is set to heatmap. Although this function can be called directly by the user, this is not recommended. The dat list contains the following items:

x

x-coordinates (in bases) along chromosome

y

intensity matrix of probes along chromosome

flag

indicates probe uniqueness in the genome. Possibilities are 3: multiple perfect matches, 2: has no PM but one or more near-matches, 1: has exactly one PM and some near-matches in the genome, 0: has exactly one PM and no near-matches.

extras

(optional) matrix of additional values (such as test-statistics/p-values) to be plotted

Author(s)

Wolfgang Huber <[e-mail]>

Examples

  data(segnf)
  data(gffSub)
  nmLabel = colnames(segnf$"1.+"@y)
  plotAlongChrom(segnf,chr=1,coord=c(35000,50000),what="heatmap", 
  		gff=gffSub,rowNamesHeatmap=nmLabel) ##using raster image

Example output

Loading required package: Biobase
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, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: pixmap
Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'

tilingArray documentation built on Nov. 8, 2020, 10:59 p.m.