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Last data update: 2014.03.03

R: Heatmap of a matrix with grouped rows and columns

groupedHeatmap

R Documentation

Heatmap of a matrix with grouped rows and columns

Description

The function uses grid.rect and grid.rect to draw a heatmap with grouped rows and columns.

Usage

groupedHeatmap(z, frow, fcol,
  fillcolours = c("#2166ac","#4393c3","#92c5de","#d1e5f0","#fefefe","#fddbc7","#f4a582","#d6604d","#b2182b"),
  bordercolour = "#e0e0e0",
  zlim = range(z, na.rm=TRUE))

Arguments

`z`	A matrix with row and column names.
`frow`	A `factor` of length `nrow(z)` indicating the row grouping.
`fcol`	A `factor` of length `ncol(z)` indicating the column grouping.
`fillcolours`	A `character` vector of colours from which the colour map is obtained through interpolation.
`bordercolour`	Either a `character` vector of length 1, specifying the border colour of the heatmap tiles, or `NULL` or `NA`, which indicates that the border colour should match the fill colour.
`zlim`	Lower and upper limit of `z` values represented in the colour map.

Details

The function can be called within other drawing operations from the grid package, e.g. within a viewport.

Value

The function is called for its side effect, drawing text and rectangles on the current viewport.

Author(s)

Wolfgang Huber http://www.ebi.ac.uk/huber

Examples


data("mtcars")

groupedHeatmap(
  scale(mtcars),
  frow = factor(sapply(strsplit(rownames(mtcars), " "), "[", 1)),
  fcol = factor(round(seq_len(ncol(mtcars))/3)))

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> library(geneplotter)
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

Welcome to Bioconductor

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

Loading required package: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: XML
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/geneplotter/groupedHeatmap.Rd_%03d_medium.png", width=480, height=480)
> ### Name: groupedHeatmap
> ### Title: Heatmap of a matrix with grouped rows and columns
> ### Aliases: groupedHeatmap
> 
> ### ** Examples
> 
> 
> data("mtcars")
> 
> groupedHeatmap(
+   scale(mtcars),
+   frow = factor(sapply(strsplit(rownames(mtcars), " "), "[", 1)),
+   fcol = factor(round(seq_len(ncol(mtcars))/3)))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>