similar to: fixing a problem in the subtree code

Hi. I did write those functions, and sent them (I thought) to one of the R maintainers to see whether they would be appropriate for inclusion (because I'd seen some requests on the mailing lists). However, I'm happy to post them -- I should have thought of it before. WARNING: I've tested these functions on some data arising in my work and also on the USArrests data that comes with

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

> I have performed clustering analysis with hclust (Ward's method) on a > database of 800 samples. As you may imagine the full dendrogram is not > really readable. I have obtained groups with cutree. I would like to plot > sub-sections of my big dendrogram to show group 1, group 2 and so on. I don't think R has anything like subtree in Splus, unfortunately. I think what has

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

Dear R community, I would like to plot a partial hclust output, so I?am looking for a subtree function that would return an tree structure I can plot. I ran the test code of subtree following the instruction on?http://finzi.psych.upenn.edu/library/extracat/html/subtree.html However, an error message popped up: ====> library(extracat) Attaching package: ?extracat? The following object is masked

Dear all, below you find enclosed my message from January 9th and my program (attention: beginner). Thanks for both answers! a. However, as far as I know the cosine is not the same as the Pearson correlation (only in special cases). b. Reid Huntsinger's hint was very useful, however I had to transpose the matrix first, for I want to calculate the distance of the _rows_. Regards, Petra

I am attempting to replicate what Cluster 3.0 and Treeview (both by Mike Eisen) to cluster both microarray genes and arrays does using R with hclust. I basically utilized the plot.mat function in sma library with some layout() and hclust(). 1. Can I know if some has already written such a function or available in some package. 2. If not, would appreciate if someone could take the time to test

Hello, a. is there a possibility to obtain a distance matrix with the cosine between vectors?? hclust, hierclust, dist will not work and seem to be hard to extend. b. if there is not: Is the cosine between vectors implemented somewhere? Thanks for all hints and advice! Petra Steiner -------------- next part -------------- An HTML attachment was scrubbed... URL:

Dear R users, There is a error message when I run the following code. It is used to load microarray data and use the top 1000 genes for training svm to classify test set . > library(e1071) Loading required package: class > f=read.table("F:\\lab\\ microarray analysis\\VEH LPS\\exprs.txt",

Hi all (really probably just Deepayan): In the plot below I want to add text on either side of each violin plot that indicates the number of observations that are either positive or negative. I'm trying to do this with ltext() and I've also monkeyed about with panel.text(). The code below is generally what I want but my calls to ltext() are wrong and I'm not sure how to fix them.

Dear community Find enclosed the full working example. Many thanks Sibylle Test_cat.csv Names Subcategory_type sources.cyto source Factor A.A material "A" A 1 B.B material "B" B 1 C.C regulation "C" C 1 D.D regulation "D" D 1 E.E habitat "E" E 1 F.F cultural "F" F 1 Test_adjac.csv

Hi, this seems to work (assuming that your problem was the setting of colours...): --- snip --- network %>% ggraph(., layout = "auto") + # This produces an error... # geom_edge_arc(curvature=0.3, aes(width=(E(network)$weight/10), color=c("darkblue", "red")[as.factor(edge_list$relationship)], alpha=0.5)) + # ... this works :-)

Dear r-help, I'm interested in finding a better way to add a column to a data frame when calculating the new column requires more than one conditional. For example, if I wanted to associate a character string in {"Pos","Neg","Zero"} with each number in the following data frame: > d <- data.frame(num = -2:2) > d num 1 -2 2 -1 3 0 4 1 5 2 I

Dear Sibylle, your example is not working! E.g. no data for "aes_collapsed". Best, Kimmo ke, 2024-03-20 kello 19:28 +0100, SIBYLLE ST?CKLI via R-help kirjoitti: > Dear community > > I am using ggraph to plot a network analysis. See part 2 in the working > example. > Besides different colors for different groups of nodes: > --> geom_node_point(aes(size =

Hello all I've been using the hclust and as.dendrogram objects for hierarchical clustering. The problem I have is that my sample set is now so large (circa 500 points) that it isn't possible to view the leaf nodes. I'd like to be able to zoom in on specific areas of the graph by selecting a region with the mouse. I've deduced from trial and error that the xlim and ylim

hello, I am using following command classify_polarity(documents,algorithm="bayes",verbose=TRUE) output is: [1] "DOCUMENT 1" [1] "WORD: excited CAT: positive POL: strongsubj SCORE: 8.44419229853175" [1] "WORD: happy CAT: positive POL: strongsubj SCORE: 8.44419229853175" [1] "WORD: optimistic CAT: positive POL: weaksubj SCORE: 7.7510451179718" [1]

Hi guys, I'm a new to R and following along with Tutorials using this book: http://www.amazon.com/Practical-Statistical-Analysis-Non-structured-Applications/dp/012386979X In one of them, they use the twitteR package and describe the following function (see below). From what I can tell from the documentation (R), there's a method to call it directly in an interactive session. The way

I'd like to change the way plot.hclust displays an hclust object. Here's a description of how it's done now, from the R documentation of hclust: In hierarchical cluster displays, a decision is needed at each merge to specify which subtree should go on the left and which on the right. Since, for n observations there are n-1 merges, there are 2^{(n-1)} possible

Dear R Helpers, I read carefully the documentation and all postings on the hclust and cutree functions, however some aspects of the tree ordering and cluster assignment performed by these functions remain unclear to me, so I would very much appreciate your help in making sure I get them right. Here is an example, with values chosen to illustrate the problems. I have a set of five profiles

I don't know the Russell-Rao coefficient but maybe this will help: You can compute the number of times y and x are both 1 (that's what your function f does) by counting 1s in y*x, i.e., sum(y*x), aka t(y)%*%x. Ordinary matrix multiplication does this row-by-column, so if M and N are two binary matrices, M%*%t(N) will have (i,j) entry equal to the count of 1s in common to row i of M and