Mark W Kimpel
2007-Sep-05 03:13 UTC
[R] problem formatting and positioning title in heatmap
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
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
--
---
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine
15032 Hunter Court, Westfield, IN 46074
(317) 490-5129 Work, & Mobile & VoiceMail
(317) 663-0513 Home (no voice mail please)
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, MarkUse 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 >