Where does one find A2Rplot that is called in that example? A2R does not appear to be on CRAN. I did find this:
http://addictedtor.free.fr/Download/A2R.zip which is a zip file containing some R code but it is not a package, which the line library(A2R) seems to need, and it does not include A2Rplot in any case. On 3/10/06, Christos Hatzis <[EMAIL PROTECTED]> wrote: > See also the colored dendrogram in the R Graph Gallery. It has a couple of > additional cool features. > > http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=79 > > > -Christos Hatzis > > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Dylan Beaudette > Sent: Friday, March 10, 2006 4:37 PM > To: [email protected] > Subject: Re: [R] coloring leaves in a hclust or dendrogram plot [solved] > > On Thursday 09 March 2006 06:12 pm, Dylan Beaudette wrote: > > Greetings, > > > > I have perused the r-help mailing list archives for an answer to this > > question, without avail. > > > > I would like to color the "leaves" of a dendrogram plot based on a > > cutoff in one of the variables involved in the initial clustering. > > > > My input data is in the form of: > > B K > > Alameda 0.2475770 0.7524230 > > Alpine 0.4546784 0.5453216 > > Amador 0.6278610 0.3721390 > > > > essentially rows labeled by county name, with two variables: percent > > voted for B and percent voted for K. While it is obvious that this is > > somewhat of a contrived example, I intend to use this as a learning > device. > > > > Here is the code used to create and plot the dendrogram: > > hc <- hclust(dist(y), "ave") > > dend <- as.dendrogram(hc) > > plot(dend, main="CA 2004 Election Results by County") > > > > An example of the output can be found here: > > http://casoilresource.lawr.ucdavis.edu/drupal/node/206?size=_original > > > > > > I have experimented with the edgePar and nodePar parameters for the > > plot.dendrogram() method, but have not been able to make sense of the > > output. > > > > The basis for setting the colors of the leaves in the dendrogram is a > > simple majority calculation: > > > > reds <- y[y$B > 0.5, ] > > blues <- y[y$K > 0.5, ] > > > > Such that leaves in the tree will be colored based on the membership > > in either of the two above groups. > > > > Is there a resource documenting how this might be accomplished? > > > > Any thoughts or ideas would be greatly appreciated. > > > > Cheers, > > > > Dylan > > Replying to my own post... > > Discovered the dendapply() function: > > reds <<- as.factor(row.names(y[y$B > 0.5, ])) blues <<- > as.factor(row.names(y[y$K > 0.5, ])) > > #define a function for coloring and sizing node elements: > colLab <- function(n) > { > if(is.leaf(n)) > { > a <- attributes(n) > if ( length(which(blues == a$label)) == 1 ) > { > attr(n, "nodePar") <- c(a$nodePar, list(lab.col = "blue", lab.cex=.7, > col="blue", cex=pop[n], pch=16 )) > } > else > { > attr(n, "nodePar") <- c(a$nodePar, list(lab.col = "red", lab.cex=.7, > col="red", cex=pop[n], pch=16)) > } > } > n > } > > #modfiy dendrogram nodes and re-plot > dend_colored <- dendrapply(dend, colLab) > > ...which did the trick > > http://casoilresource.lawr.ucdavis.edu/drupal/node/210 > > > > -- > Dylan Beaudette > Soils and Biogeochemistry Graduate Group University of California at Davis > 530.754.7341 > > ______________________________________________ > [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 > > ______________________________________________ > [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 > ______________________________________________ [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
