search for: nodepar

..."ave") (dend1 <- as.dendrogram(hc)) # "print()" method str(dend1) # "str()" method str(dend1, max = 2) # only the first two sub-levels op <- par(mfrow= c(2,2), mar = c(5,2,1,4)) plot(dend1) ## "triangle" type and show inner nodes: plot(dend1, nodePar=list(pch = c(1,NA), cex=0.8, lab.cex = 0.8), type = "t", center=TRUE) plot(dend1, edgePar=list(col = 1:2, lty = 2:3), dLeaf=1, edge.root = TRUE) plot(dend1, nodePar=list(pch = 2:1,cex=.4*2:1, col = 2:3), horiz=TRUE) dend2 <- cut(dend1, h=70) plot(dend2$upper) ## leafs are wrong...

...h R. I followed the example shown in http://stat.ethz.ch/R-manual/R-devel/library/stats/html/dendrogram.html dist.obj <- as.dist(matrix.distance) hc.obj <- hclust(dist.obj,method="ave") dend1 <- as.dendrogram(hc.obj) plot(hc.obj, xlab='',ylab='',sub='', nodePar=list(pch = c(1,NA), cex=0.8, lab.cex = 0.8)). But I got warning and the plot does not look like what I wanted. Warning messages: In plot.hclust(hc.obj, xlab = "", ylab = "", sub = "", nodePar = list(pch = c(1, : "nodePar" is not a graphical parameter...

...would be a useful feature to have.... Or is there an easier way of doing this that I have missed? Walton Green * * * my.dend.plot <- function (x, type = c("rectangle", "triangle"), center = FALSE, edge.root = is.leaf(x) || !is.null(attr(x, "edgetext")), nodePar = NULL, edgePar = list(), leaflab = c("perpendicular", "textlike", "none"), dLeaf = NULL, xlab = "", ylab = "", xaxt = "n", yaxt = "s", horiz = FALSE, frame.plot = FALSE, twig.col = NULL, lab.col = NULL, leaf.col = NU...

...our the leaves according to the predicted group, or some other variable. The obvious thing to try is plot(stuff.hc, col=c("red","green","blue")[stuff.predicted.group]) but that doesn't work. I read everything that seemed plausible, and came across nodePar, but col <- c("red","green","blue")[stuff.predicted.group] plot(stuff.hc, nodePar=list(col=list("black",col))) tells me repeatedly that parameter "nodePar" couldn't be set in high-level plot() function while plo...

...<<- function(n) { if(is.leaf(n)) { a <- attributes(n) crm <- as.numeric(a$label) gene <- as.character(bm[which(bm$CRM_ID==crm),5]) color <- as.character(gene2color[which(gene2color$genes==gene),2]) i <<- i+1 attr(n, "nodePar") <- # c(a$nodePar, list(lab.col = my_colors[i], lab.font= i%%3)) c(a$nodePar, list(lab.col = color)) } n } my_colors <- grDevices::rainbow(attr(dhc,"members")) i <- 0 }) dL <- dendrapply(dhc, colLab) op <- par(mfrow=2:1) plot...

Dear all, i performed a clusteranalysis - which worked so far... i plotted the dendrogram and sooo many branches, a rough sketch would be enough ;) i tried max.levels therefore which worked, but not for the plot... i used the following plot(hcd,nodePar =nP, str(hcd,max.level=1)) the output on the terminal was: --[dendrogram w/ 2 branches and 196 members at h = 2.70] |--[dendrogram w/ 2 branches and 34 members at h = 1.79] .. `--[dendrogram w/ 2 branches and 162 members at h = 1.95] .. which is great ! but i cant get it done for the plot...

...luster) res = as.dendrogram(agnes(data)) chlab <- function(n) { if(is.leaf(n)) { att <- attributes(n) labx <- data$category1[att$label] lab_color <- ifelse(labx == "A", "black", ifelse(labx == "B", "red", "green")) attr(n, "nodePar") <- c(att$nodePar, lab.col = lab_color, pch = NA) attr(n, "label") <- labx } n } # lab.col = lab_color, res2 = dendrapply(res, chlab) print(res2) pdf("dendrogram.pdf",width=5,height=2.5,pointsize=8,paper='special') par(mai=c(0.5,0.5,0.2,0.2)) plot(res2)...

...cript(1) were not the distances defined in my distance matrices. script: var<-read.table("the distance matrix i calculated", header=TRUE, sep=" ") var_HC<-hclust(as.dist(var),method="average") var_dendro<-as.dendrogram(var_HC) plot(var_dendro,ylim=c(0,5), nodePar =list(lab.cex = 0.3), header=title(" My Distance Matrix")) I did some research and found that the hclust function (from the hclust help page): "...Initially, each object is assigned to its own cluster and then the algorithm proceeds iteratively, at each stage joining the two most...

Hello, a. when I use hclust with the methods media, centroid, and mcquitty, and plot the results, the dendrograms have lines that are crossing each other. Is this ok? b. My next question refers to plot.dendrogram: How can I use parameters as "hang" or "cex" here? E.g. for st <- as.dendrogram(subtreeshc[[x]]) I would like to have something like this, where cex and hang

Dear List RGui Version : 2.3.0 User : 1 month I am having the *dendrogram plotting problem * The code i tried: >library(cluster) DD<-DataSetS01022 # 575 x 2 matrix > VC<-hclust(dist(DD),"ave") *Warning message: NAs introduced by coercion* ( what does it mean? Is that the problem?) > plot(VC,hang=-2) Output: http://roughjade.blogspot.com Can anyone guide me? Thanks

Hello everyone, I wanted to know if it was possible to change the color of certain leaves in a hclust object in order to make my graph more readable. I know I can color certain groups but I would like to enter a vector telling the plot function which leaves to color in which color. Thanks in advance, Eleni [[alternative HTML version deleted]]

...quot;2" 5.962963 "3" 0.473462 "4" 0.682300 R code: hc<-hcluster(m, link="ave") dhc<-as.dendrogram(hc) dendrapply(dhc, function(n) str(attributes(n))) local({ colLab <<- function(n){ if(is.leaf(n)){ a <- attributes(n) i <<- i+1 attr(n, "nodePar") <- c(a$nodePar, list(lab.col = mycols[i], lab.font=i%%3)) } n } #mycols <- grDevices::rainbow(attr(dhc,"members")) i <- 0 }) dL <- dendrapply(dhc, colLab) plot(dL) ------------------------------------------------------------- On 12/26/06, r-help-request@stat.math.ethz...

...that names are preserved. o data.frame(check.names = TRUE) (the default) enforces unique names, as S does. o .Defunct() now has 'new' and 'package' arguments like those of .Deprecated(). o The plot() method for "dendrogram" objects now respects many more nodePar and edgePar settings and for edge labeling computes the extents of the diamond more correctly. o deparse(), dput() and dump() have a new 'control' argument to control the level of detail when deparsing. dump() defaults to the most detail, the others default to less. See ?.deparseO...

...that names are preserved. o data.frame(check.names = TRUE) (the default) enforces unique names, as S does. o .Defunct() now has 'new' and 'package' arguments like those of .Deprecated(). o The plot() method for "dendrogram" objects now respects many more nodePar and edgePar settings and for edge labeling computes the extents of the diamond more correctly. o deparse(), dput() and dump() have a new 'control' argument to control the level of detail when deparsing. dump() defaults to the most detail, the others default to less. See ?.deparseO...

...tions can now read from concatenated bzip2 files (including files written with bzfile(open = "a")) and files created by some other compressors (such as the example of PR#14479). ? The primitive function c() is now of type BUILTIN. ? plot(<dendrogram>, .., nodePar=*) now obeys an optional xpd specification (allowing clipping to be turned off completely). ? nls(algorithm="port") now shares more code with nlminb(), and is more consistent with the other nls() algorithms in its return value. ? xz has been updated to 5.0.1 (v...

...tions can now read from concatenated bzip2 files (including files written with bzfile(open = "a")) and files created by some other compressors (such as the example of PR#14479). ? The primitive function c() is now of type BUILTIN. ? plot(<dendrogram>, .., nodePar=*) now obeys an optional xpd specification (allowing clipping to be turned off completely). ? nls(algorithm="port") now shares more code with nlminb(), and is more consistent with the other nls() algorithms in its return value. ? xz has been updated to 5.0.1 (v...