Re: [R] heatmap aspect ratio
You can change the code of layout: layout(lmat, widths = lwid, heights = lhei, respect = TRUE) layout(lmat, widths = lwid, heights = lhei, respect = FALSE) (best to create a new function my.layout with the modified code) Jacob Michaelson wrote: Hi all, Does anyone know of a fairly easy way to stretch a heatmap vertically? I've got 42 arrays and would like to be able to see as many significant genes as possible (right now I can only get 50 genes with it still being readable). In some comparisons there are several hundred significant genes. I've fiddled with the asp argument, but that doesn't give the results I'm looking for -- only scales the images, not the dendrograms. Is there any way to make the heatmap rectangular rather than square without hacking the heatmap function itself (which is where I'm headed next)? Thanks in advance, Jake __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] 2d plotting and colours
And does this work? n - 5 par(mfrow = c(2,2)) palette(default) barplot(1:25,col = 1:25) pal - rainbow(n) barplot(1:25,col = pal[(1:25-1)%%n+1]) pal - rgb((0:15)/15, g=0,b=0, names=paste(red,0:15,sep=.)) barplot(1:25,col = pal[(1:25-1)%%n+1]) Earl F. Glynn wrote: Mulholland, Tom [EMAIL PROTECTED] wrote in message news:[EMAIL PROTECTED] Since I was only concentrating on colour issues and not on your specific problem I was just showing the possibilities. Does this code help n - 5 par(mfrow = c(2,2)) palette(default) barplot(1:25,col = 1:25) palette(rainbow(n)) barplot(1:25,col = 1:25) palette(rgb((0:15)/15, g=0,b=0, names=paste(red,0:15,sep=.))) barplot(1:25,col = 1:25) require(cluster) x - runif(100) * 8 + 2 cl - kmeans(x, n) palette(rainbow(n)) plot(x, col = cl$cluster) abline(h = cl$centers, lty = 2,col = grey ) palette(palette()[order(cl$centers)]) points(x,col = cl$cluster,pch = 20,cex = 0.4) Using Windows with R 2.0.1 this looks fine at first. But when I resize the graphic, copy the graphic to a metafile and paste it into Word, or go to an earlier graphic and come back using History, the colors ae all messed up. It's as if only the last palette is being used for all four plots in the figure. Oddly, if I copy the graphic as a bitmap, the colors are preseved in the bitmap. Is this a quirk of my machine or does this happen for others? Is it possible that the Windows palette manager is being used (which is such about obsolete) and that true color graphics are not being used (which is the easist way to avoid headaches from the Windows palette manager)? efg __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] PlotML
Dear all, Has anybody ever written some plot / hist functions that would return PlotML code? [http://ptolemy.eecs.berkeley.edu/] Regards, Gregoire __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] PlotML
Has anybody ever written some plot / hist functions that would return PlotML code? [http://ptolemy.eecs.berkeley.edu/] http://ptolemy.eecs.berkeley.edu/%5D Not that I know of, and looking at the design of PlotML, it doesn't look like a nice fit as an R device driver. PlotML works at the level of data sets, bar graphs, axes, etc., not with low-level items like lines, polygons, and text. There are general XML handling tools in the XML package, though. Thx. I've wrapped up a couple of functions into a package that does what I need. In case somebody is interested I've put it with an example at: http://penyfan.ugent.be/ptplot/ . Note that you might also need to install R2HTML. Regards, Gregoire __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] hclust title and paste - messed up
paste(c(a,b,c),collapse=)
paste(a,b,c,sep=)
On Mon, 2004-10-11 at 13:40, Dan Bolser wrote:
I use the following code to scan a (limited) parameter space of clustering
strategies ...
data - read.table(...
dataTranspose - t(data)
distMeth - c(euclidean,
maximum,
manhattan,
canberra,
binary
)
clustMeth - c(ward,
single,
complete,
average,
mcquitty,
median,
centroid
)
par(ask=TRUE)
for (d in distMeth){
print(d)
dt - dist(dataTranspose,method=d)
for (m in clustMeth){
print(m)
hc - hclust(dt,method=m)
plot(hc,
main=paste(c(
Distance Measure, d,
Cluster Method, m),sep= ),
xlab='',
sub=''
)
}
}
However, my plot title (main) has 4 lines, when I think it should only
have one line.
What am I doing wrong?
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