Plot Heatmaps

Description

Plots a heatmap with clustering of rows and columns specified by the rowGroups and colGroups, respectively.

Usage

myHeatmap2(x, rowGroups = factor(rep(1, nrow(x))), colGroups = factor(rep(1, ncol(x))), keeprownames = TRUE, colors = colorRampPalette(brewer.pal(9, "Blues")[-1])(100), ...)

Arguments

Value

The result of the function is a plot.

Author(s)

Wolfgang Huber, 2013

See Also

myHeatmap

Examples

## The function is currently defined as
function (x, rowGroups = factor(rep(1, nrow(x))), colGroups = factor(rep(1, ncol(x))),
    keeprownames = TRUE, colors = colorRampPalette(brewer.pal(9, "Blues")[-1])(100), ...) {
    x = ordermat(x, rowGroups, ...)
    x = ordermat(t(x), colGroups, ...)
    if (!keeprownames) 
        colnames(x) = NULL
    print(levelplot(x, aspect = "fill", xlab = "", ylab = "", 
        scales = list(x = list(rot = 90), raster = TRUE), col.regions = colors, 
        colorkey = list(space = "left", height = 0.15, useRaster = TRUE)))
  }

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(Hiiragi2013)
Loading required package: affy
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

Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: boot
Loading required package: clue
Loading required package: cluster
Loading required package: genefilter
Loading required package: geneplotter
Loading required package: lattice

Attaching package: 'lattice'

The following object is masked from 'package:boot':

    melanoma

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
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:IRanges':

    space

The following object is masked from 'package:S4Vectors':

    space

The following object is masked from 'package:stats':

    lowess

Loading required package: gtools

Attaching package: 'gtools'

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

    inv.logit, logit

Loading required package: KEGGREST
Loading required package: MASS

Attaching package: 'MASS'

The following object is masked from 'package:AnnotationDbi':

    select

The following object is masked from 'package:genefilter':

    area

Loading required package: mouse4302.db
Loading required package: org.Mm.eg.db


Loading required package: RColorBrewer
Loading required package: xtable
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Hiiragi2013/myHeatmap2.Rd_%03d_medium.png", width=480, height=480)
> ### Name: myHeatmap2
> ### Title: Plot Heatmaps
> ### Aliases: myHeatmap2
> 
> ### ** Examples
> 
> ## The function is currently defined as
> function (x, rowGroups = factor(rep(1, nrow(x))), colGroups = factor(rep(1, ncol(x))),
+     keeprownames = TRUE, colors = colorRampPalette(brewer.pal(9, "Blues")[-1])(100), ...) {
+     x = ordermat(x, rowGroups, ...)
+     x = ordermat(t(x), colGroups, ...)
+     if (!keeprownames) 
+         colnames(x) = NULL
+     print(levelplot(x, aspect = "fill", xlab = "", ylab = "", 
+         scales = list(x = list(rot = 90), raster = TRUE), col.regions = colors, 
+         colorkey = list(space = "left", height = 0.15, useRaster = TRUE)))
+   }
function (x, rowGroups = factor(rep(1, nrow(x))), colGroups = factor(rep(1, 
    ncol(x))), keeprownames = TRUE, colors = colorRampPalette(brewer.pal(9, 
    "Blues")[-1])(100), ...) 
{
    x = ordermat(x, rowGroups, ...)
    x = ordermat(t(x), colGroups, ...)
    if (!keeprownames) 
        colnames(x) = NULL
    print(levelplot(x, aspect = "fill", xlab = "", ylab = "", 
        scales = list(x = list(rot = 90), raster = TRUE), col.regions = colors, 
        colorkey = list(space = "left", height = 0.15, useRaster = TRUE)))
}
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>