similar to: Manually modifying an hclust dendrogram to remove singletons

I am having difficulty getting the dynamic tree cut package to work. Given the data table "myddtable" LengthPlaceColorAge5HRed224ABlue205WGreen243GRed222GBlue236WGreen255ARed194H Blue23 I created a similarity matrix using DAISY and Gower metric and specified Place and Color columns as characters (since they are categorical variables) > dd.daisy<-daisy(myddtable, metric =

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

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

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 "Branch 1" (h=

I am trying to learn how to format Ascii data files for scan or read into R. Precisely for a quickie project, I found some code (at end of this email) to do exactly what I need: To cluster and graph a dendrogram from package (stats). I am stuck on how to format a text file to run the script. I looked at the dataset USArrests (which would be replaced by my data and labels) using UltraEdit. That

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

Good afternoon, After cuting a hierarchical tree using cutree(), how to check correspondances between classes and branches? This is what we do: srndpchc <- hclust(dist(srndpc$x[1:1000,1:3]),method="ward") #creation of hierarchical tree plclust(srndpchc,hmin=20000) #visualisation srndpchc20000 = cutree(srndpchc,h=20000) #returns 4 classes table(srndpchc20000 ) srndclass20000 =

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, it would be nice to be able to specify workers as singletons. By this I mean that every call to the new_worker method returns the same instance of said worker. This can be done transparently either by adding a new argument to new_worker (something like :singleton => true) or adding a new method, like I did in my installation of BackgrounDrb: def get_worker_by_class(klass)

I am having difficulty getting the dynamic tree cut package to work. Given the data table "myddtable" LengthPlaceColorAge5HRed224ABlue205WGreen243GRed222GBlue236WGreen255ARed194H Blue23 I created a similarity matrix using DAISY and Gower metric and specified Place and Color columns as characters (since they are categorical variables) > dd.daisy<-daisy(myddtable, metric =

Hi, I have a controller where I access a singleton class that I use to connect to a DRbprocess DrbConnector.instance.some_method I notice that on every request, the constructor is called so it is making a new instance of this singleton. Is this normal? Thanks, Curtis

Hello all, just started tinkering with Rails after reading all the hype about it. I''m a raw novice with Ruby and (obviously) Rails, but have extensive experience with serverside Java (J2EE stack, Tapestry, etc). Rails looks cool, though embedding Ruby code in HTML reminds me unpleasantly of JSP + Struts and I''m deeply suspicious of all the behind-the-scenes magic going on in

A bug (misfeature) has been found in the S gee library (and thus in the R gee library). The problem, which is shared by nearly all gee implementations, involves the calculation of working correlations when some clusters have only one observation. For compatibility reasons nearly everyone uses the computing formula from the first SAS macro by Karim, rather than the formula from the original GEE

Hello, I've been clustering my data using hclust and cutting the resulting tree with cutree. Separately, I visualize the clusterings with heatmap. Is it possible to have the dendrogram on the heatmap reflect the cutree results? That is, instead of having one large dendrogram, it would have 4 or 25 in the example below. Any guidance on if that's possible or not, and what kinds of

How can I safely mock a singleton without the mocked method living on outside the scope of the test method? I''ve run into this problem with mocking methods on globals (gasp!) in the past by doing something like def mock_my_global original = $my_global $my_global.expects(:foo).returns(''bar'') yield $my_global = original end Is there something similar I

As part of my project to put different types of results into worksheets, I would like to be able to put an auto-generated methods section. If I compose in RWinEdt, read into R, and use write.table with a .txt file extension, what I get out has line-breaks that correspond to those I put in in the first place. If I do the same thing but write.xls with .xls extention, I get an Excel worksheet

Hi All, i've problem to understand how to work with R to generate a hierarchical clustering my data are in a csv and looks like : idcode,count,temp,sal,depth_m,subs 16001,136,4.308,32.828,63.46,47 16001,109,4.31,32.829,63.09,49 16001,107,4.302,32.822,62.54,47 16001,87,4.318,32.834,62.54,48 16002,82,4.312,32.832,63.28,49 16002,77,4.325,32.828,65.65,46 16002,77,4.302,32.821,62.36,47

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 all, I know it may not have much sense thinking about a Singleton Pattern in an R application which doesn't use any OOP facilities, however I'm curious to know if anybody faced the same issue. I've been googling but using "singleton pattern" as a key word leads to typical OOP languages like Java or C++ among others. So my problem is that I'd like to ensure some very

Gang- 1. Is there anything in Ruby that handles the .properites files similar to the J2EE application servers. Or do I need to define all of the properties as constants? 2. Is there anyway I can load some of my classes (such as singletons) during the startup? I am looking for the startup classes that J2EE containers provide. Thanks -- Posted via http://www.ruby-forum.com/.