similar to: Rotating dendrograms

Hello all, I wish to compare two dendrograms (representing Hierarchical Clusterings). My problems are several: 1) how do I manually create a dendrogram object ? That is, how can I reconstruct it as an "hclust" object that creates such a dendrogram, when all I have is the dendrogram image (but don't have the underlaying distance matrix that produced it) ? I see that there is a

Hi, I'm using the latticeExtra package's dendrogramGrob function to create a grob with both a dendrogram and a covariate bar (via the 'add' parameter). When the dendrogram has very short branches at its leaves, it appears as a line and becomes impossible to see when placed next to the covariate bar. For example: > x <- outer(-5:5, -5:5, "*") + matrix(nrow = 11,

Hello fellow R users, I am currently learning to use R, so please forgive me if there is an obvious explanation for the following problem. My goal is to perform WGCNA on a dataset of 19776 genes, so I opted to follow the block-wise network construction (Section 2c) in the WGCNA R Tutorial by Peter Langfelder and Steve Horvath. I ended up with 10 blocks and am able to plot the dendrograms and

Hi, I have produced a dendrogram of categorical data in R using the hclust function, although the input was a dissimilarity matrix produced in SAS, as I have defined my own distances. The dendrogram is fine and I can view and use this. However, I was wondering if there is a method by which I can find out the optimal place to place groups, rather than relying on my visual analysis? I don't

Dear all, Does anyone know how to rotate a dendengram? My purpose is to put a dendrogram on top of an image plot and then put a rotated dendrogram on the left hand side (LHS) of the image plot. The image plot represents a matrix and each node of the top (LHS) dendrogram will correspond to each column (row) of matrix. Thanks, Ming-Chung Li

I would like to be able to exert certain types of control over the plotting of dendrograms (representing hierarchical clusterings) that I think is best achieved by modifying the dendrogram object prior to plotting. I am using the "dendrogram" class and associated methods. Define the cluster number of each cluster formed as the corresponding row of the merge object. So, if you are

Hi, I'm trying to build dendrograms to pass to heatmap(). The dendrograms I build plot properly, but when I pass them to heatmap() I get the error message "row dendrogram ordering gave index of wrong length" (see output log below). I looked in the code of heatmap() and saw that the error was due to a NULL return value from order.dendrogram(), which in turn got a NULL return value

I'd like to be able to cut dendrograms at a height I specify and then plot the resulting subtrees. I wanted to use the dendrogram object for this purpose because there doesn't seem to be a canned way to cut a hclust object and get a list of hclust objects, but there is a function (cut) that does that for dendrograms. The problem I'm having is that when I plot a dendrogram, I

I am using hclust and plot to produce dendrograms. Using my input data I am able to complete an analysis and obtain a vertical plot. I want to be able to plot the dendrogram horizontally.I am using version 2.6 of R and have updated my packages recently. Using the sample script for dendrograms I can produce a horizontal plot using the instruction horiz = TRUE in plot(). When I use the same

I am trying to create a dendrogram object to be able to display a multiway table. I understand how the dendrogram object is structured, a nested list of lists, but I am having trouble trying to create that structure from a table. Basically, what I would like to do is pass a multiway table, say table(a,b,c) to a function and have it display the table as a dendrogram. If a,b,c, and d are all

Hi, I have an hclust object say hcl with heights starting from a negative and ending to a positive value. I would like to rotate the plot(hcl) 90 degrees clockwise. It is suggested to use plot(as.dendogram(hcl), horiz=T) but I encountered two problems: 1) a dendrogram object does not accept negative heights 2) horiz=T rotates the tree 90 degrees unclockwise any ideas? thanks, Vahid PARTOVI

Good afternoon, I ran heatmap and hclust on the same matrix x (strictly, I ran heatmap(x), and hclust(dist(t(x))), and realized that the two dendrograms were slightly different, in that the left-right arrangement of one pair of subclusters (columns) was reversed in the two functions (but all individual columns were grouped correctly). Looking through the code for heatmap as a most definite

Hi all, I would like to color code the leaves on a dendrogram to reflect group membership. Does anyone know of a function to do this besides code listed at http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=79? I haven't seen anything recently to accomplish this. I basically just want to color code sample (leaf) labels. Thanks for any help. Wade

Hello all, I am using libraries (mva,cluster) to produce dendrograms. With 1000 examples the dendrogram gets too crowded, and i am wondering whether there is an option (which i cannot find) to set the number of leaf nodes, like in matlab, and return the plot and the assignment map examples -> leaf nodes. Any suggestion is appreciated. Thanks Edo

Hallo everybody, I have a question concerning plotting of hclust dendrograms. I created several of those dendrograms and like to plot them in different plots. I'd like to have all plots with the same scaling of the y axis so that they become comparable by eye. That means they should all start at y=0 and end up with a certain given value, e.g. y=8. I tried the following: plot(

Dear R-users, I need some help concerning the plotting of dendrograms for hierarchical agglomerative clustering. The agglomeration niveau of each step should be displayed at the branches of the dendrogram. For this I need the x/y coordinates of the branch-agglomerations of the dendrogram. The y-values are known (the heights of the agglomeration), but how can I get the x-values? > mydata

Dear list, I am trying to plot a radial dendrogram using the ape package, which requires my data to be of class 'phylo'. Currently I have my dendrogram stored as an object of class 'dendrogram' which was produced from an outside bit of C code, but was made into an object of class 'igraph.eigenc' and converted to a dendrogram using 'as.dendrogram()' from the igraph

Dear all, I am using the heatmap representations of latticeExtra package and I would be interested to draw color side bars representing the groups of a factor of interest. From my understanding of : > help(dendrogramGrob) ... The 'add' argument can be used for additional annotation at the base of the dendrogram. It should be a list with one component for each row,

Hello, I would like to display a heatmap with dendrograms and allow the user to click on either dendrogram to choose a sub-dendrogram. The function heatmap() uses layout() and image() and the plot method of dendrogram to plot the heatmap and dendrograms, but if locator() is then called and the user clicks, the coordinates returned from locator() are with respect to the last thing plotted (e.g.,

Hi all, I'm having a problem where by I'm trying to use the NeatMap draw.dendrogram function as it is more versatile in placement/direction of dendrograms, instead of the limited plot function. Using plot I can get my dendrograms to display the species name for each leaf of the tree. But I cannot figure out how to make this happen using draw.dendrogram.. genetic<-