search for: dend1

Dear r-list, I am trying to visually seperate the two main clusters of a dendrogram. The idea is to use: 'edgePar=list(lty=3)' for 'dend1[[1]]' and 'edgePar=list(lty=1)' for 'dend1[[2]]' I have not found a way to solve this. Any suggestions? Patrick hc <- hclust(dist(USArrests), "ave") (dend1 <- as.dendrogram(hc)) par(mfrow=c(2,2)) plot(dend1) plot(dend1[[1]],edgePar=list(lty=3)) plot(dend1[[2]]...

...gram each one with a different colour. How can I do? I guess I could do using *edgetext* and then *t.col* or* lab.col* but I don't know how to add edgetext to my dendrogram. Can you help me please? Example: require(graphics); require(utils) hc <- hclust(dist(USArrests), "ave") (dend1 <- as.dendrogram(hc)) plot(dend1) labels (USArrests) [[1]] # to know how many cities (labels) = 50 nP <- list(col=3:2, cex=c(2.0, 0.75), pch= 21:22, bg= c("light blue", "pink"), lab.cex = 0.75, lab.col = 1:50) # or use a palette: palette(rainbow(50))...

...c(4.7,3.1)) plot(pts, xlim = c(0,6), ylim = c(0,4),type = "n", xlab = "Feature 1", ylab = "Feature 2") points(pts,pch = as.character(1:5)) ## build a hierarhical tree, store as a dendrogram aggTree <- hclust(dist(pts), method = "single") (dend1 <- JB.as.dendrogram.hclust(aggTree)) ## NOTE: only thing I added to official version of ## as.dendrogram.hclust: ## each node has an attribute cNum, which gives ## the merge step at which it was formed, ## i.e. gives the row of the merge object which ## describes the formation of that node ## on...

...ct. Can someone explain why my script does not work. Sample code follows: ----------------------------------------------------------------------- # Sample code extracted from the Dendrogram documentation in R # require(graphics); require(utils) hc <- hclust(dist(USArrests), "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, horiz = TRUE) plot(dend1) # # My code # x <- read.table("Rclust2.data",he...

Hi! In the example: hc <- hclust(dist(USArrests), "ave") dend1 <- as.dendrogram(hc) dend2 <- cut(dend1, h=70) Do the branches "Branch 1", "Branch 2", "Branch 2"...in dend2$upper str(dend2$upper) --[dendrogram w/ 2 branches and 4 members at h = 152] |--[dendrogram w/ 2 branches and 2 members at h = 77.6] | |--leaf...

...6 0.051 5/31/1996 0.016 0.000 0.045 6/30/1996 0.015 0.051 0.054 7/31/1996 0.014 0.098 -0.027 8/31/1996 0.013 -0.034 0.036 9/30/1996 0.011 -0.059 0.016 10/31/1996 0.014 0.043 0.017 11/30/1996 0.014 -0.029 0.026 Code Example from Help files: hc <- hclust(dist(USArrests), "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,N...

...different labels of my dendrogram. How can I do? I guess I could to using *edgetext* and then* t.col* or *lab.col* but I don't know how to add edgetext to my dendrogram. Can you help me please? Example: require(graphics); require(utils) hc <- hclust(dist(USArrests), "ave") plot(dend1) labels (USArrests) [[1]] # to know how many cities (labels) = 50 nP <- list(col=3:2, cex=c(2.0, 0.75), pch= 21:22, bg= c("light blue", "pink"), lab.cex = 0.75, lab.col = 1:50) # or use a palette: palette(rainbow(50)) plot(dend1, edgePar=nP, dLeaf=1, e...

Hello, It seems that the plot function for dendrograms does not draw labels when they are too long. > hc <- hclust(dist(USArrests), "ave") > dend1 <- as.dendrogram(hc) > dend2 <- cut(dend1, h=70) > dd <- dend2$lower[[1]] > plot(dd) # first label is drawn > attr(dd[[1]], "label") <- "aaaaaaaaaaaaaaaaaa" > plot(dd) # first label is NOT drawn Is this expected ? Is it possible to force the drawing ?...

...rent color and want the leaves laying down bottom. The script like this. I am not familiar with 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 =...

...39;m having is that when I plot a dendrogram, I can't figure out how to add labels to the nodes. For example, this example from the dendrogram documentation plots a dendrogram without labels: library(mva) data(USArrests) hc <- hclust(dist(USArrests), "ave") str(dend1 <- as.dendrogram(hc)) plot(dend1) dend2 <- cut(dend1, h=70) plot(dend2$upper) plot(dend2$lower[[3]]) So... does anyone know how to cut an hclust object and get a list of hclust objects, or how to plot a dendrogram object with labels? Thanks. David Marimont NXP Dat...

I have done a cluster analysis doing: 1-clusNorth <-hclust(dist(Artorious)^2, method="ward") 2-clusNorth$labels <-Artorious$Name ## to show the case names and not numbers 3-dend1 <- as.dendrogram(clusNorth) 4-plot(dend1) My Dendrogram is now showing the names of my cases in the dataframe on the x axis 1 OMNICELL INC COM 2 GETTY IMAGES INC COM 3 INTERCONTINENTALEXCHANGE IN COM 4 OPTIONSXPRESS HLDGS INC COM 5 SU...

...!is.na(mat$count) & !is.na(mat$subs),] distmat<-vegdist(dd) clusa<-hclust(distmat,"average") print(clusa) Call: hclust(d = distmat, method = "average") Cluster method : average Distance : bray Number of objects: 8036 print(dend1 <- as.dendrogram(clusa)) 'dendrogram' with 2 branches and 8036 members total, at height 0.3194225 dend2 <- cut(dend1, h=0.07) a complete run with plots is available here : http://nbviewer.ipython.org/5492912 i'm trying try to group together the species (idcode's) that...

Hi When I use plot(hclust(dist..)...)...) etc to create a dendrogram of a hierarchial cluster analysis, I end up with a vertical tree. What do I need to do to get a horizontal tree? Also, my users are used to seeing trees who's leaves all "end" at the same place (eg. Like in minitab). Is this possible in R? Thanks Mick Michael Watson Head of Informatics Institute for Animal

...sing list at the same time. In dendrogram-speech I basically would like the label of the leaf and the height of the enclosing branch. A dendrogram example (from the help file of stats::dendrogram), and some functions showing how it is structured: hc <- hclust(dist(USArrests), "ave") dend1 <- as.dendrogram(hc) plot(dend1) str(dend1) Similarly to dendrapply(), I tried o recursively obtain from the tree a list including, for each member (leaf) the height of the list containing it. However, I fail to fully grasp how the 'recursiveness' is made within the function saving both...

Dear R-Help, I have a clustering problem with hclust that I hope someone can help me with. Consider the classic hclust example: hc <- hclust(dist(USArrests), "ave") plot(hc) I would like to cut the tree up in such a way so as to avoid small clusters, so that we get a minimum number of items in each cluster, and therefore avoid singletons. e.g. in this example, you can see