plotHeatmap: plots a heatmap for an interaction screen.

In RNAinteract: Estimate Pairwise Interactions from multidimensional features

Description

A heatmap of an interaction screen is plotted.

Usage

plotHeatmap(sgi, screen, channel, pi.max = NULL,
            main = expression(paste(pi, "-score")),
	    hc.row = NULL, hc.col = NULL, 
	    withoutgroups = c("neg", "pos"))

Arguments

sgi	An object of class RNAinteract
screen	The screen name of which the interaction matrix is plotted.
channel	The channel name of which the interaction matrix is plotted.
pi.max	The pairwise interaction score that is represented at the top of the color scale. All interaction scores above this value can not be distinguished any more.
main	The title of the plot.
hc.row	A hierarchical clustering (hclust) for the rows.
hc.col	A hierarchical clustering (hclust) for the columns.
withoutgroups	The genes within this group are not shown in the heatmap. It is convinient to hide screen controls in the heatmap.

Details

A heatmap for one screen and one channel is plotted. Positive interactions are marked blue, negative ones are marked yellow. A colorbar is shown on the left hand side.

Value

Returns a grob.

Author(s)

Bernd Fischer

See Also

RNAinteract-package

Examples

data("sgi")
plotHeatmap(sgi, screen="1", channel="nrCells")

Example output

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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

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

Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'

RNAinteract documentation built on Nov. 8, 2020, 5:28 p.m.