[R] problem formatting and positioning title in heatmap

[Uwe Ligges]

Mark W Kimpel wrote:
> I am using heatmap with the arguments below. The title size stays the 
> same no matter what I set cex.main to. Is this expected? Can I adjust 
> the title size in heatmap?
> 
> Also, the position of the main title is at the very upper edge of the 
> output and if I use a "\n" to stack the title the upper line is out of 
> bounds and doesn't show up.
> 
> I am outputting to pdf.
> 
> Any help? Thanks, Mark


Use par() to set that parameter of the device as in:

par(cex.main=1)
heatmap(.....)

Uwe Ligges


> heatmap(x = dataM, RowSideColors = RowSideColors, 
> ColSideColors=ColSideColors, main = title,
>            margins = c(50,50), scale= do.scale ,labRow=geneNames, 
> labCol=colLabels, col = hmcol, cex.main = 1,
>            cexRow = row.lab.mag, cexCol = col.lab.mag)
> 
>  > sessionInfo()
> R version 2.6.0 Under development (unstable) (2007-08-29 r42686)
> i686-pc-linux-gnu
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> [8] methods   base
> 
> other attached packages:
>   [1] RColorBrewer_1.0-1     MergeMaid_2.9.0        MASS_7.2-36
>   [4] rat2302_1.17.0         rat2302cdf_1.17.0      affycoretools_1.9.4
>   [7] annaffy_1.9.1          KEGG_1.17.1            GO_1.99.1
> [10] xtable_1.5-1           gcrma_2.9.1            matchprobes_1.9.10
> [13] biomaRt_1.11.4         RCurl_0.8-3            XML_1.92-1
> [16] GOstats_2.3.16         Category_2.3.30        genefilter_1.15.11
> [19] survival_2.32          RBGL_1.13.6            annotate_1.15.6
> [22] GO.db_1.99.1           AnnotationDbi_0.1.12   RSQLite_0.6-0
> [25] DBI_0.2-3              limma_2.11.11          affy_1.15.7
> [28] preprocessCore_0.99.12 affyio_1.5.8           Biobase_1.15.30
> [31] graph_1.15.14
> 
> loaded via a namespace (and not attached):
> [1] cluster_1.11.7
>