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Last data update: 2014.03.03

R: A heatmap grob

grid.sgiHeatmap

R Documentation

A heatmap grob

Description

A grob is created and printed for a matrix PI which is intended to represent pairwise interaction scores.

Usage

grid.sgiHeatmap(PI, pi.max = NULL, main = expression(paste(pi, "-score")), 
		hc.row = NULL, hc.col = NULL)

Arguments

`PI`	A matrix of pairwise interactions.
`pi.max`	The interaction score at the top end of the colorbar. pairwise interaction score larger than this value can not be distinguished anymore.
`main`	A title for the plot.
`hc.row`	An hierarchical clustering as produced by hclust of the rows.
`hc.col`	Clustering of the columns.

Details

A heatmap is plotted with positive interaction represented in yellow and negative interactions represented in blue. A colorbar is plotted on the left and dendrograms are added. This function can be used to integrate the plot in other grid objects. It is recommended to use the function plotHeatmap to plot heatmaps of an RNAinteract object.

Value

A grob is returned.

Author(s)

Bernd Fischer

Examples

data("sgi")
PI = getData(sgi, type="pi", format="targetMatrix", screen="1", channel="nrCells")
grid.sgiHeatmap(PI)

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(RNAinteract)
Loading required package: abind
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RNAinteract/grid.sgiHeatmap.Rd_%03d_medium.png", width=480, height=480)
> ### Name: grid.sgiHeatmap
> ### Title: A heatmap grob
> ### Aliases: grid.sgiHeatmap
> ### Keywords: hplot
> 
> ### ** Examples
> 
> data("sgi")
> PI = getData(sgi, type="pi", format="targetMatrix", screen="1", channel="nrCells")
> grid.sgiHeatmap(PI)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>