plot.annHeatmap: Plotting method for annotated heatmaps

In Heatplus: Heatmaps with row and/or column covariates and colored clusters

Description

Plotting method for annotated heatmaps

Usage

    ## S3 method for class 'annHeatmap'
plot(x, widths, heights, ...)

Arguments

x	an object of class annHeatmap
widths	a numerical vector giving the widths of the sub-plots currently defined
heights	a numerical vector giving the heights of the sub-plots currently defined
...	extra graphical parameters, currently ignored

Details

This function displays an annotated heatmap object that has been previously generated by annHeatmap2 or on of its wrappers. The arguments widths and heights work as in layout.

Value

x, invisibly returned. If widths or heights have been specified, they overwrite the corresponding items x$layout$width and x$layout$height in x.

See Also

annHeatmap2, heatmapLayout, layout

Examples

    ## Define the map
    require(Biobase)
    data(sample.ExpressionSet)
    ex1 = sample.ExpressionSet[51:85,]
    map1 = annHeatmap2(exprs(ex1), ann=list(Col=list(data=pData(ex1))),
                   cluster=list(Col=list(cuth=3000)))
    
    ## Plot it               
    plot(map1)
    
    ## More heatmap, smaller dendrogram/annotation
    map2 = plot(map1, heights = c(1,6,1))
    
    ## Compare layout before/after
    with(map1$layout, layout(plot, width, height))
    layout.show(4)
    with(map2$layout, layout(plot, width, height))
    layout.show(4)

Example output

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, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

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    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Heatplus documentation built on Nov. 8, 2020, 6:24 p.m.