Complete Linkage Clustering

Jaya has asked for the wisdom of the Perl Monks concerning the following question:

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Re: Complete Linkage Clustering by kvale (Monsignor) on Feb 27, 2005 at 01:05 UTC
For complete linkage clustering and other hierarchical clustering methods, check out Algorithm::Cluster, a Perl binding to the C Cluster library. -Mark	[reply]
Re^2: Complete Linkage Clustering by Jaya (Acolyte) on Feb 27, 2005 at 05:21 UTC
Thank You! I have installed the Algorithm::Cluster module. I have a very large distance matrix to solve. The function Algorithm::Cluster::treecluster(%param) seems to cluster genes or microarray. `%param=( data => \@m, #Wanted array reference, but got a #reference to . mask =>'', #Parameter 'mask' is not a valid #matrix, ignoring it. weight =>'', #Parameter 'weight' does not point #to an array, ignoring it. transpose = '', #Parameter 'transpose' must be #either 0 or 1 (got '') )` [download] I have stated the errors against its corresponding statements. Any suggestion? Thanks Edit by BazB: remove excess code tags.	[reply] [d/l]
Re^3: Complete Linkage Clustering by punkish (Priest) on Feb 27, 2005 at 14:24 UTC
Hmmm... usually folks ask questions about why their program isn't working. You already seem to understand why it isn't working. I have no idea what "complete linkage clustering" is, but you have already provided the errors above... so fix 'em and you will be on your way. In particular, 'weight' is pointing to an empty string... change it to an array as required. 'transpose' is pointing to an empty string... change it to 0 or 1. 'mask' is pointing to an empty string. Correct that. 'data' seems to be ok... it _is_ pointing to an arrayref... check @m and see if it is what the program expects. -- when small people start casting long shadows, it is time to go to bed	[reply]
Re^4: Complete Linkage Clustering by Jaya (Acolyte) on Feb 27, 2005 at 16:20 UTC
Re: Complete Linkage Clustering by chanio (Priest) on Feb 27, 2005 at 20:52 UTC
It seems to be just an interface to the C library, so you should read the cluster.pdf manual to know the way of expressing your knowledge in the programmer's way. Then, read the Perl module. Please, see the Open Cluster site. .{\('v')/} C H E E R U P ! _`(___)' ___a_l_b_e_r_t_o_________ Wherever I lay my KNOPPIX disk, a new FREE LINUX nation could be established.	[reply]
Re^2: Complete Linkage Clustering by Jaya (Acolyte) on Feb 27, 2005 at 22:29 UTC
Thank you. I have managed to get the cluster output. My questions seem trivial. I am bit new to Perl. I was wondering if there is any module to represent the cluster output into dendrogram. I checked the search.CPAN to find if there are any modules for graphical representation of the cluster . But I could not find any. They are all for Bioclusters. I need to represent the result in graphical form. Since there is a module to obtain the clustering result,is there any module to represent this result in graphical(dendrogram) format? `($result, $linkdist) = Algorithm::Cluster::treecluster(%param);` [download] Thanks for all the help.	[reply] [d/l]
Re: Complete Linkage Clustering by Jaya (Acolyte) on Feb 28, 2005 at 02:17 UTC
I was wondering if there is any module to represent the cluster output into dendrogram. I checked the search.CPAN to find if there are any modules for graphical representation of the cluster . But I could not find any. They are all for Bioclusters. I need to represent the result in graphical form. Since there is a module to obtain the clustering result,is there any module to represent this result in graphical(dendrogram) format? `($result, $linkdist) = Algorithm::Cluster::treecluster(%param);` [download] Thanks for all the help.	[reply] [d/l]