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Last data update: 2014.03.03

R: Display Data as Heatmap

metaheat

R Documentation

Display Data as Heatmap

Description

This function displays a matrix as a heatmap. It is based on function heatmap_2 in the Heatplus package.

Usage

metaheat(x, Rowv = NA, Colv = NA, distfun = dist, hclustfun = hclust, na.rm = TRUE, do.dendro = c(TRUE, TRUE), legend = 0, legfrac = 8, col = heat.colors(12), r.cex = NULL, c.cex = NULL, ...)

Arguments

`x`	the numerical data matrix to be displayed
`Rowv`	either a dendrogram or a vector of reordering indexes for the rows, setting to `NA` suppresses re-ordering of rows
`Colv`	either a dendrogram or a vector of reordering indexes for the columns, setting to `NA` suppresses re-ordering of columns
`distfun`	function to compute the distances between rows and columns. Defaults to `dist`
`hclustfun`	function used to cluster rows and columns. Defaults to `hclust`
`na.rm`	logical indicating whther to remove NAs
`do.dendro`	logical vector of length two, indicating (in this order) whether to draw the row and column dendrograms
`legend`	integer between 1 and 4, indicating on which side of the plot the legend should be drawn: 1=bottom, 2=left, 3=above, 4=right
`legfrac`	fraction of the plot that is taken up by the legend; larger values correspond to smaller legends
`col`	the color scheme
`r.cex`	font size for row labels
`c.cex`	font size for column labels
`...`	extra arguments to `image`

Author(s)

Ivana Ihnatova

Examples

lists<-list(Method1=c("Gene_A", "Gene_V","Gene_S","Gene_C","Gene_U","Gene_D","Gene_E","Gene_G","Gene_W"), 
  Method2=c("Gene_D","Gene_W","Gene_G","Gene_E","Gene_H","Gene_X"),
  Method3=c("Gene_L","Gene_K","Gene_J","Gene_M","Gene_V","Gene_T","Gene_R","Gene_U"))
A<-make.matrix(lists)
metaheat(A, legend=1, col=c(3,4))

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(MAMA)
Loading required package: genefilter
Loading required package: metaMA

Attaching package: 'metaMA'

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

    rowVars

Loading required package: xtable
Loading required package: multtest
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: gtools
Loading required package: grid
Loading required package: GeneMeta

Attaching package: 'MAMA'

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

    multExpFDR, zScoreFDR, zScorePermuted, zScores

> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/MAMA/metaheat.Rd_%03d_medium.png", width=480, height=480)
> ### Name: metaheat
> ### Title: Display Data as Heatmap
> ### Aliases: metaheat
> ### Keywords: hplot
> 
> ### ** Examples
> 
> lists<-list(Method1=c("Gene_A", "Gene_V","Gene_S","Gene_C","Gene_U","Gene_D","Gene_E","Gene_G","Gene_W"), 
+   Method2=c("Gene_D","Gene_W","Gene_G","Gene_E","Gene_H","Gene_X"),
+   Method3=c("Gene_L","Gene_K","Gene_J","Gene_M","Gene_V","Gene_T","Gene_R","Gene_U"))
> A<-make.matrix(lists)
> metaheat(A, legend=1, col=c(3,4))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>