similar to: processing data of hierarchical river network

Displaying 20 results from an estimated 10000 matches similar to: "processing data of hierarchical river network"

2010 Feb 21
1
How to: Compare Two dendrograms (Hierarchical Clusterings) ?
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
2012 Feb 23
2
Advice on exploration of sub-clusters in hierarchical dendrogram
Dear R user, I am a biochemist/bioinformatician, at the moment working on protein clusterings by conformation similarity. I only started seriously working with R about a couple of months ago. I have been able so far to read my way through tutorials and set-up my hierarchical clusterings. My problem is that I cannot find a way to obtain information on the rooting of specific nodes, i.e. of
2010 May 25
1
Hierarchical clustering using own distance matrices
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",
2011 Jul 27
0
Inversions in hierarchical clustering were they shouldn't be
Hi, I''m using heatmap.2 to cluster my data, using the centroid method for clustering and the maximum method for calculating the distance matrix: library("gplots") library("RColorBrewer") test <- matrix(c(0.96, 0.07, 0.97, 0.98, 0.50, 0.28, 0.29, 0.77, 0.08, 0.96, 0.51, 0.51, 0.14, 0.19, 0.41, 0.51), ncol=4, byrow=TRUE)
2013 May 01
1
help understanding hierarchical clustering
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
2008 Mar 08
1
Elbow criterion plots for determining k in hierarchical clustering
Hi There, I'm working on some cluster analyses on a large data-set using hclust with Wards method and Manhattan (city block) distance measures. I've created dendrograms to illustrate the clustering criteria, but would like to create a plot to examine for the classic elbow criterion to use in determining the best number of clusters. Ideally I'd like to plot percent variance explained
2006 Aug 15
1
Hierarchical clustering
Hi, I'm new to R; this is my second email to this forum. I have a dataset that looks like this: Gene A B C D A 511 6116 1515 1515 B 164 115 1515 494 C 21646 D
2008 Feb 11
1
Dendrogram for agglomerative hierarchical clustering result
Hey group, I have a problem of drawing dendrogram as the result of my program written in C. My algorithm is a approximation algorithm for single linkage method. AS a result I will get the following data: [Average distance] [cluster A] [cluster B] For example: 42.593141 1 26 42.593141 4 6 42.593141 123 124 42.593141 4 113 74.244206 1 123 74.244206 4 133 74.244206 1 36 So far I have used C to
2012 Mar 08
2
hierarchical clustering of large dataset
Hello All, i've a set of observations that is in the form : a, b, c, d, e, f 67.12, 4.28, 1.7825, 30, 3, 16001 67.12, 4.28, 1.7825, 30, 3, 16001 66.57, 4.28, 1.355, 30, 3, 16001 66.2, 4.28, 1.3459, 13, 3, 16001 66.2, 4.28, 1.3459, 13, 3, 16001 66.2, 4.28, 1.3459, 13, 3, 16001 66.2,
2005 Dec 01
1
R Hierarchical clustering leaf node
Hello, I am new to the R package. After I use R to perform the hierarchical clustering, I am only interested in retrieving the leaf nodes that share the last common ancestors. As illustrated below, I'd like to retrieve (B, C) as a cluster and then (D, E) as another cluster. Any chance to do this in R? Thanks! BTW, I just subscribed to this list (not sure if the subscription is
2000 Aug 18
0
J. River (makers of Media Jukebox) interested in helping with development...
Hello everyone, This is Matt Ashland, a developer for J. River, the makers of the popular freeware program Media Jukebox. (some of you may know me better as the author Monkey's Audio). Our development team here at J. River is quite interested in helping with the development of Ogg Vorbis. The licensing restrictions of other formats (namely mp3) are becoming somewhat problematic for us,
2012 Aug 12
0
Different cluster orderings from cutree() and cut.dendrogram()
Hi! I just discovered that cutree() and cut.dendrogram() do not assign the same cluster numberings when called on the same tree. More specifically, cutree() assigns cluster numbers by order of appearance in the data, while cut.dendrogram() sorts clusters by height (see example below). I guess this is for historical reasons? I'm hit by this difference when I want to get a vector of cluster
2005 Nov 02
1
x/y coordinates of dendrogram branches
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
2003 Sep 08
1
graphic of hierachical clustering
Hi all, I would like to save the dendrogram of a hierarchical clustering. Let reshc the result of the fucntion hclust(). To save the dendrogram, I can use the function postscript: postscript(file="hc605.ps") plot(as.dendrogram(reshc),horiz=T,ylab="",main=" ") dev.off() Using the functions plot and as.dendrogram, it is possible to obtain an horizontal tree with
2007 Apr 25
1
heatmap and phylogram / dendogram ploting problem, ape package
I am having trouble displaying a dendrogram of evolutionary relationships (a phylogram imported from the ape package) as the vertical component of a heatmap, but keeping the hierarchical clustering of the horizontal component. The relationships of the vertical component in the generated heatmap are not that of the dendrogram, although the ordering is. In more detail, I am attempting to generate
2012 Jun 28
0
neatmap - draw.dendrogram - help!
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<-
2006 Feb 28
1
creating dendrogram from cluster hierarchy
Dear R users, I have created data for hierarchical agglomerative cluster analysis which consist of the merging pairs and the agglomeration heights, e.g. something like my.merge <- matrix(c(-1,-2,-3,1), ncol=2, byrow=TRUE) my.height <- c(0.5, 1) I'd like to plot a corresponding dendrogram but I don't know how to convert my data to achieve this. Is it possible to create a
2005 Jul 11
1
indexing into and modifying dendrograms
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
2002 May 14
0
RE: cut.dendrogram (PR#1552)
>>>>> "MikG" == M GRUM <M.GRUM@CGIAR.ORG> writes: MikG> I'm resending this bug report with a new example. As MikG> seen below, cut.dendrogram gives an error message for MikG> some heights, but not for others and with some MikG> datasets adn not others. I can't see why. MikG> Last time I unwittingly sent my message with
2010 May 20
2
Overlap of leaf labels
Hi, I have tried looking at the archives but havent found any answer that works till now (Sorry if i have missed anything) I am a newbie to R and i am trying to carry out hierarchical clustering using hclust -> as.dendrogram and then plotting the results as a dendrogram using the plot function plot(object). My question is : In the function "plot", can one decrease the leaf label