similar to: Help on hclust and viewing the results as PDF and JPEG please

Hi everyone, I've been opening up R 2.0.1 from the dock and then starting the Mac OSX X11 server. After that I call >jpeg("test.jpg",plot(rnorm(10))) and r pops up a quartz window with the appropriate graph in it and puts a file called test.jpg into the HOME which is 0kb in size and is completely empty. There is no error message. I've tried >png("test.png",

Hi I cannot seem to create any files that have the name "CON" before the file extension, i.e. all of the following fail: > pdf("CON.pdf") Error in pdf("CON.pdf") : unable to start device pdf > jpeg('CON.jpeg') Error in jpeg("CON.jpeg") : unable to start device devWindows > png('CON.png') Error in png("CON.png") : unable

I've been using the hclust() function in R to generate a hierarchial tree as graphical output. However, with large datasets, it's impossible to decipher the output because all the labels are superimposed. Is it possible to generate a numerical representation (as opposed to a diagram) of the ouput from hclust? I'd like to use it for large datasets of up to 20,000 rows. Thanks in

Dear R community, I am trying to understand how the ward linkage works from a quantitative point of view. To test it I have devised a simple 3-members set: G = c(0,2,10) The distances between all couples are: d(0,2) = 2 d(0,10) = 10 d(2,10) = 8 The smallest distance corresponds to merging 0 and 2. The corresponding ESS are: ESS(0,2) = 2*var(c(0,2)) = 4 ESS(0,10)

Dear List, Some days ago, it was posted in this list a question regarding "How to generate graphics (jpeg) files dynamically". Although it was responded, there is a particular case in which I do not find the rigth solution. My question also goes in the same direction but for the particular case of generating jpeg/bmp or png files when using xyplot (grid/lattice libraries) and the

Hello, I would like to cut a hclust tree into several groups at a specific similarity. I assume this can be achieved by specifying the "h" argument with the specified similarity, e.g.: clust<-hclust(dist,"average") cut<-cutree(clust,h=0.65) Now, I would like to draw rectangles around the branches of the dendrogram highlighting the corresponding clusters, as is done by

Hello, how can I get the similarity value (i.e., the inner cluster similarity) that was used to cut a hierarchical tree at a specific height? I would appreciate your help! Best regards, Madeleine

Hello, I will really appreciate some help with the following question. let's say cor.m is a correlation coefficient matrix. tree<-hclust(as.dist(1-cor.m)); plot(tree); my question is: is it possible to add the correlation coefficient information to the plot? thanks, S. Ma

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

I am making heatmaps for a dataset (~ 300*600 matrix) with the following R script (I am not familiar with R and this is the first time I am using it). library("gplots") library("Cairo") mydata <- read.csv(file="data.csv", header=TRUE, sep=",") rownames(mydata)=mydata$Name mydata <- mydata[,2:297] mydatamatrix <- data.matrix(mydata) mydatascale

Full_Name: Ivan Egorov Version: 1.8.1 OS: MS Windows 2000, SP4 Submission from: (NULL) (194.186.91.129) V<-t(matrix(scan('C:/V3.dat'),3)) d<-dist(V) hc<-hclust(d) rect.hclust(hc,5) Error message is displayed: Read 24 items Error in rect(m[which[n]] + 0.66, par("usr")[3], m[which[n] + 1] + 0.33, : plot.new has not been called yet Here's my data file

Dear List, My dataset is as below: I am using library(cluster) hierarchical clustering on these data. If i try to plot these i couldn't see the partitions clearly, > dd<-hclust(dist(DataSetS01022Full), "ave") > Warning message: >NAs introduced by coercion >(dn<-as.dendrogram(dd)) >plot(dn) please find the link on the plot : http://roughjade.blogspot.com

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 have the following code that perform hiearchical clustering and plot them in heatmap. __ library(gplots) set.seed(538) # generate data y <- matrix(rnorm(50), 10, 5, dimnames=list(paste("g", 1:10, sep=""), paste("t", 1:5, sep=""))) # the actual data is much larger that the above # perform hiearchical clustering and plot heatmap test <- heatmap.2(y)

Hi, I'm doing hierarchical clustering, and want to export my dendrogram to a tree-viewing/editing software. I can do this by converting the data to Newick format (hc2Newick in ctc package), but I can't get branch lengths to show in the resulting phylogram. I figured it might help to convert my hclust object into a phylo object (as.phylo in ape package), but the following lines give me

Hi all, This is the first time I'm writing to R-devel, and this time I'm just asking for the purpose for a certain line of code in stats::as.hclust.dendrogram, which comes up as I'm trying to fix dendextend. The line in question is at line 128 of dendrogram.R in R-3.3.3, at stats::as.hclust.dendrogram: stopifnot(length(s) == 2L, all( vapply(s, is.integer, NA) )) Is there any

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 =

Dear all, The default plotting method for hclust trees looks just fine for few objects like in the example dataset. But when it comes to many features (eg some 1000 and more - I'm trying to visualize clustered microarray data) it renders a tree, that one cannot inspect, because of overlapping text and lines. My question is, is there a way or a plotting parameter for plotting a tree which is

I have a report I need to generate from posted form data with the optional choice of also generating a pdf of the same report. I am wondering if it is possible to do both, display the report in the page AND also generate the PDF data, within the same action, ie, user selects all the info they want in the report, also selecting ''Generate PDF'', submits form and report is displayed

Hi R-users, Maybe my last question was not specified enough to get a lot of answers, so I'm trying to do a new attempt: I use R 2.6.2 and Windows XP. I've got the following question: I wrote a lot of text into the margin of a plot. I have to take the borders of the graphics device and enlarge the plot to get a "clean" image. By default the plot and the table on the right side