heatmapGenome: clustering and heatmap
In snapCGH: Segmentation, normalisation and processing of aCGH data

Description Usage Arguments Details See Also

This function clusters samples and shows their heatmap

heatmapGenome(input, response = as.factor(rep("All", ncol(input))),
                 chrominfo = chrominfo.Mb, cutoff = 1, lowCol =
                 "blue", highCol = "yellow", midCol = "white", ncolors =
                 50, byclass = FALSE, showaber = FALSE, amplif = 1,
                 homdel = -0.75, samplenames = colnames(input),
                 vecchrom = 1:22, titles = "Image Plot", methodS =
                 "ward", categoricalPheno = TRUE, CENTROMERE = FALSE)

`input`	object of class `MAList` or `SegList`
`response`	phenotype of interest. defaults to the same phenotype assigned to all samples
`chrominfo`	a chromosomal information associated with the mapping of the data
`cutoff`	maximum absolute value. all the values are floored to +/-cutoff depending on whether they are positive of negative. defaults to 1
`ncolors`	number of colors in the grid. input to `maPalette`. defaults to 50
`lowCol`	color for the low (negative) values. input to `maPalette`. defaults to "red"
`highCol`	color for the high (positive) values. input to `maPalette`. defaults to "green"
`midCol`	color for the values close to 0. input to `maPalette`. defaults to "black"
`byclass`	logical indicating whether samples should be clustered within each level of the phenotype or overall. defaults to F
`showaber`	logical indicating whether high level amplifications and homozygous deletions should be indicated on the plot. defaults to F
`amplif`	positive value that all observations equal or exceeding it are marked by yellow dots indicating high-level changes. defaults to 1
`homdel`	negative value that all observations equal or below it are marked by light blue dots indicating homozygous deletions. defaults to -0.75
`samplenames`	sample names
`vecchrom`	vector of chromosomal indeces to use for clustering and to display. defaults to 1:23
`titles`	plot title. defaults to "Image Plots"
`methodS`	clustering method to cluster samples. defaults to "ward"

`categoricalPheno`	logical indicating whether phenotype is categorical. Continuous phenotypes are treated as "no groups" except that their values are dispalyed.defaults to TRUE.
`CENTROMERE`	logical indicating whether to plot the centromere

This functions is a more flexible version of the heatmap. It can cluster within levels of categorical phenotype as well as all of the samples while displaying phenotype levels in different colors. It also uses any combination of chromosomes that is requested and clusters samples based on these chromosomes only. It draws the chromosomal boundaries and displays high level changes and homozygous deletions. If phenotype if not categorical, its values may still be displayed but groups are not formed and byclass = F. Image plot has the samples reordered according to clustering order.

heatmap

snapCGH documentation built on Nov. 8, 2020, 5:31 p.m.