similar to: Coloring leaves in Dendrogram according to gene names

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

Hi all, I am a real novice to R. :) I am struggling with a problem for generating colored dendrogram. I have searched the R list and complied/collected a R code which can generated a colored dendrogram based on the rainbow color and 4x4 similarity matrix (say matrix:m). In this dendrogram, each leaf is colored differently. But, I do not want the leaf colored on a random basis. I want to assign

Dear R-help list, I'd like to create visualize the clustering of a dataset with a dendrogram. I'm using the following script: data = read.table("data.csv", header=T, sep=";") require(cluster) res = as.dendrogram(agnes(data)) chlab <- function(n) { if(is.leaf(n)) { att <- attributes(n) labx <- data$category1[att$label] lab_color <- ifelse(labx ==

Dear R Users, I am writing code to present my output data (I'm using Lattice Package). However, it's essential for me to control space between barchart and legend. I've read the package's specification, but unfortunately I haven't spot the information how to do this. Here's the code I've written: barchart(mymatrix[,1:ncol(mymatrix)],horizontal=FALSE,

Core developers, I couldn't find any simple way to send a vector of colors to apply to each terminal in plot.dendrogram() or plot.hclust()---I asked R-help about it a few weeks ago and didn't get any response---so I hacked that functionality into the plot.dendrgram code (see below for hacked function plus examples).... Is there any chance this functionality could be added to the

Hi I have a distance matrix which is computed by user defined method. I would like to plot the dendrogram. I would like to use different 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 <-

Dear I am using the 'as.dendrogram' function from the 'stats' library to convert from an hclust object to a dendrogram with a dataset of size ~30000 (an example code is below). I need the dendrogram structure to use the "dendrapply" and "attributes" functions and to access the child nodes, I do not need any of the plot properties. The problem is that it

I have a data set with 6 variables and 251 cases. The people who supplied me with this data set believe that it falls naturally into three groups, and have given me a rule for determining group number from these 6 variables. If I do scaled.stuff <- scale(stuff, TRUE, c(...the design ranges...)) stuff.dist <- dist(scaled.stuff) stuff.hc <- hclust(stuff.dist)

Hi, I have been trying unsuccessfully to plot data using different colors based on a variable within a subset of an imported file. The file I am reading is about 20000 lines long and has a column (in the example called FILE) that contains approximately 100 unique entries. I would like to plot a subset of the data from the file and key the color from the FILE column, This is what my file looks like

I am running centos 5.2 i686. The /boot/config indicates that VIA82CXXXX is built into the kernel. CONFIG_BLK_DEV_VIA82CXXX=y my lspci -v gives 00:0f.0 IDE interface: VIA Technologies, Inc. CX700M2 IDE (prog-if 8a [Master SecP PriP]) Subsystem: VIA Technologies, Inc. Unknown device 0581 Flags: bus master, medium devsel, latency 32 I/O ports at fc00 [size=16]

Dear all, i performed a clusteranalysis - which worked so far... i plotted the dendrogram and sooo many branches, a rough sketch would be enough ;) i tried max.levels therefore which worked, but not for the plot... i used the following plot(hcd,nodePar =nP, str(hcd,max.level=1)) the output on the terminal was: --[dendrogram w/ 2 branches and 196 members at h = 2.70] |--[dendrogram w/ 2

Hey Everyone! I wanted to carry out Hierarchical clustering using distance matrices i have calculated ( instead of euclidean distance etc.) I understand as.dist is the function for this, but the distances in the dendrogram i got by using the following script(1) were not the distances defined in my distance matrices. script: var<-read.table("the distance matrix i calculated",

I would really like some help with understanding the panel function, in zoo. Thank you. R 15.1 and zoo 1.7-7. library(zoo) x = seq(0,3*pi,length.out=100) y = sin(x) zobj = zoo(y, x) ########################################################### ## EXAMPLE 1 - GLOBAL ARGUMENT ## This panel function works ## But, it relies on mycol, which is a global variable

I am also running a pretty recent version albeit not today's CVS, but CVS-HEAD-11/20/04-11:29:52. D you have problems b/w the Ciscos or only when going out to the PSTN?? I have 35 7960s with a PRI and no problems that you speak of. I do get an occational dropped call but that may be the DHC server lease running out on the phones. Can you tell us a little more about your setup???

If your remotes are not reporting any trouble. This may be farfetched but power may be to blame. I have had the ciscos 'freak out' with unstable power. It looks like the load on the power cubes cannot keep the caps loaded to deal with fluctuations. Or you may have a ground loop somewhere. Are the phones plugged into UPSs? I had flaky 7960 work fine after pluged into a Cisco POE switch.

This will be it for tonight... Sep 3 20:35:30 homebase dhcpd: DHCPDISCOVER from 02:97:09:02:23:a2 (cubieboard2) via eth0 Sep 3 20:35:31 homebase dhcpd: DHCPOFFER on 192.168.192.21 to 02:97:09:02:23:a2 (cubieboard2) via eth0 Sep 3 20:35:31 homebase dhcpd: /usr/local/sbin/dhcp-dyndns.sh: line 17: /var/log/dyndns.log: Permission denied Sep 3 20:35:31 homebase dhcpd:

Is IPv6 supported by PXELINUX? With the transition to IPv6 occurring already, I'm seeing requests for supporting an IPv6-Based PXEboot and need to know if it's supported or is planned for support.

Dear List RGui Version : 2.3.0 User : 1 month I am having the *dendrogram plotting problem * The code i tried: >library(cluster) DD<-DataSetS01022 # 575 x 2 matrix > VC<-hclust(dist(DD),"ave") *Warning message: NAs introduced by coercion* ( what does it mean? Is that the problem?) > plot(VC,hang=-2) Output: http://roughjade.blogspot.com Can anyone guide me? Thanks

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

Hello everyone, I wanted to know if it was possible to change the color of certain leaves in a hclust object in order to make my graph more readable. I know I can color certain groups but I would like to enter a vector telling the plot function which leaves to color in which color. Thanks in advance, Eleni [[alternative HTML version deleted]]