[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] 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] 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

[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