[R] dendrogram rect.hclust() not working?

I have tried to use rect.hclust() to draw a rectangle around a set of leaves, but am running into trouble. The rect.hclust() is drawing two rects instead of one, and of the wrong size: scoreClusterObj <- hclust(scoreDistanceObj, method=clustMethod) order <- scoreCluster

[R] lattice levelplot axis + custom annotations

How would I set the "scales" property of a lattice levelplot, so that I can add specific annotations at specific positions? For example, I have a 200 x 1000 element levelplot. Along the y-axis (along the 1000-element axis) I would like to add annotations on the left side of the levelplot at

Re: [R] lattice levelplot axis + custom annotations

On May 2, 2009, at 5:08 PM, David Winsemius wrote: Not sure since you have not provided a reproducible example and not really defined what "annotations" means. By annotations, I mean that I want to draw an object (set of poiygon() elements that make up a genomic sequence logo), anchored at

[R] rgl and axes3d() labels

I am making an rgl-based 3d plot. It works fine, except when I try to remove axis value labels and tick marks with axes3d(labels=FALSE, ticks=FALSE): --- rgl.open() offset <- 50 par3d(windowRect=c(offset, offset, 1280+offset, 1280+offset)) rm(offset) rgl.clear() rgl.viewpoi

Re: [R] rgl and axes3d() labels

xed in a future release! -Alex On Wed, Apr 23, 2014 at 5:34 PM, Duncan Murdoch wrote: > On 23/04/2014, 7:51 PM, Alex Reynolds wrote: > >> I am making an rgl-based 3d plot. It works fine, except when I try to >> remove axis value labels and tick marks with ax

Re: [R] rgl and axes3d() labels

Or perhaps the documentation could be updated to clear up what works and what doesn't. It seems pretty confusing to put options in the docs that do not work as described. -Alex > On Apr 24, 2014, at 4:05 AM, Duncan Murdoch wrote: > >> On 23/04/2014, 9:02 PM, Al

[R] How do I order xyplot line points?

I have the following xyplot figure: http://img577.imageshack.us/img577/686/filesizeresults1200.png The data are organized in a matrix file as follows: Type ElementsChromosome Time bedGz 1200chr114.240 bedGz 1200chr27.949 bedGz 1200

Re: [R] How do I order xyplot line points?

Perfect, thanks! On Nov 7, 2010, at 4:59 AM, baptiste auguie wrote: > Hi, > > try this, > > xyplot(Time~Chromosome|factor(Elements), > data = mtx[order(mtx$Chromosome), ], ... [snipped]) > > > HTH, > > baptiste > > > > >

[R] cor.test() running out of memory on 64-bit system

I am running into resource issues with calculating correlation scores with cor.test(), on R 2.13.0: R version 2.13.0 (2011-04-13) ... Platform: x86_64-unknown-linux-gnu (64-bit) In my test case, I read in a pair of ~150M vectors from text files using the pipe() and scan() functions, which p

[R] levelplot + cut() for custom color palette

I have the following data as input, from which I would like to make a lattice levelplot: - x y level 1 m3134 m3134 1.000 2 m3134 m416B 0.4189057 3 m416B m3134 0.2696508 4 m3134 mA20 0.3322170 5 mA20 m3134 0.2454191 6 m3134mB 0.3176792 ...

[R] Color bins for lattice levelplot

I am creating a levelplot figure with the following code. This should be repeatable code, which includes a link to the data I am working with. --- pdfFn <- "foo.pdf" df <- read.table("http://dl.dropbox.com/u/31495717/stackoverflow.overlaps.list.txt";, sep="\t", header=FA

[R] stretching text vertically

I'd like to stretch a plotted character vertically, to create a "sequence logo". Is there a parameter to allow stretching text() output vertically or squeeze horizontally? I know about Oliver Bembom's seqLogo library, but this generates a sequence logo plot using a separate bitmap device. I

[R] Choice of notch size in R

Is there a way to modify the choice of notch size [1] in R's boxplot routine from outlining a 5% significance region, to say 1% or lower? Thanks, Alex [1] McGill, Tukey, and Larsen. "Variations of Box Plots", The American Statistician, Vol. 32, No. 1, 12-16. _

Re: [R] Choice of notch size in R

Many thanks to you and Peter Dalgaard for your advice. Instead of notches on a classic box plot, I have elected to draw a more "minimalized" box plot along the lines suggested by Tufte, and overlap a custom significance region on this. As a statistical question, if I log-transform my data, can

[R] Dendrogram label size

Is it possible to resize the labels in a dendrogram without applying circles and triangles to edges? I tried cex.labels: plot(scoreDendogramObj, horiz=TRUE, axes=FALSE, cex.labels=0.8) but that didn't have any effect. Thanks, Alex __ R-help@r-pro

[R] Fitting long names in boxplot

ly (not the boxplot) or shrinking the names text (I tried cex.names=0.7 but this didn't help). Thanks for any advice, I apologize if these are stupid questions, -Alex -- Alex Reynolds University of Washington Medical Genetics 2211 Elliot Seattl