clmorder(1) [debian man page]
clm order(1) USER COMMANDS clm order(1) NAME clm order - reorder clusterings conformal to inclusion structure clmorder is not in actual fact a program. This manual page documents the behaviour and options of the clm program when invoked in mode order. The options -h, --apropos, --version, -set, --nop are accessible in all clm modes. They are described in the clm manual page. SYNOPSIS clm order [-prefix <string> (file multiplex prefix)] [-o <fname> (concatenated output in single file)] <cluster|stack>+ DESCRIPTION Given a set of input clusterings clm order first transform it into a stack of strictly nesting clusterings. It does this by splitting clus- ters where necessary. It then reorders the coarsest (i.e. level-one) clustering, from large to small clusters. After that it reorders the second coarsest clustering conformally such that the first batch among its reordered clusters covers the level-one largest cluster, the sec- ond batch covers the level-one second largest cluster, and so on. Within these constraints, each batch of second-level clusters (correspond- ing to a single first-level cluster) is again ordered from larger to smaller clusters. This process is applied recursively throughout the entire stack of input clusters. The input can be specified in multiple files, and a single file may contain multiple clusterings. The output is by default written as a con- catenation of matrix files, the so-called stack format. Use the -o option to specify the output file. The stacked format can be converted to Newick format using mcxdump(1). The output can be written to multiple files, one for each projected clustering, by using the -prefix option. By example, -prefix P leads to output in files named P1, P2, ..PN, where N is the number of clusters in the input, P1 is the most fine- grained ordered clustering, and PN is the coarsest clustering. OPTIONS -prefix (<string>) -o (<fname>) As decribed above. AUTHOR Stijn van Dongen. SEE ALSO mclfamily(7) for an overview of all the documentation and the utilities in the mcl family. clm order 12-068 8 Mar 2012 clm order(1)
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clm mate(1) USER COMMANDS clm mate(1) NAME clm mate - compute best matches between two clusterings clmmate is not in actual fact a program. This manual page documents the behaviour and options of the clm program when invoked in mode mate. The options -h, --apropos, --version, -set, --nop are accessible in all clm modes. They are described in the clm manual page. SYNOPSIS clm mate [-o fname (output file name)] [-b (omit headers)] [--one-to-many (require multiple hits in <clfile1>)] [-h (print synopsis, exit)] [--apropos (print synopsis, exit)] [--version (print version, exit)] <clfile1> <clfile2> DESCRIPTION clm mate computes for each cluster X in clfile1 all clusters Y in clfile2 that have non-empty intersection and outputs a line with the data points listed below. overlap(X,Y) # 2 * size(meet(X,Y)) / (size(X)+size(Y)) index(X) # name of cluster index(Y) # name of cluster size(meet(X,Y)) size(X-Y) # size of left difference size(Y-X) # size of right difference size(X) size(Y) projection(X, clfile2) # see below projection(Y, clfile1) # see below The projected size of a cluster X relative to a clustering K is simply the sum of all the nodes shared between any cluster Y in K and X, duplications allowed. For example, the projected size of (0,1) relative to {(0,2,4), (1,4,9), (1,3,5)} equals 3. The overlap between X and Y is exactly 1.0 if the two clusters are identical, and for nearly identical clusterings the score will be close to 1.0. All of this information can also be obtained from the contingency matrix defined for two clusterings. The [i,j] row-column entry in a con- tigency matrix between to clusterings gives the number of entries in the intersection between cluster i and cluster j from the respective clusterings. The other information is implicitly present; the total number of nodes in clusters i and j for example can be obtained as the sum of entries in row i and column j respectively, and the difference counts can then be obtained by substracting the intersection count. The contingency matrix can easily be computed using mcx; e.g. mcx /clfile2 lm /clfile1 lm tp mul /ting wm will create the contingency matrix in mcl matrix format in the file ting, where columns range over the clusters in clfile1. The output can be put to good use by sorting it numerically on that first score field. It is advisable to use a stable sort routine (use the -s option for UNIX sort) From this information one can quickly extract the closest clusters between two clusterings. OPTIONS -o fname (output file name) Specify the name of the output file. -b (omit headers) Batch mode, omit column names. --one-to-many (require multiple hits in <clfile1>) Do not output information for clusters in the first file that are subset of a cluster in the second file. AUTHOR Stijn van Dongen. SEE ALSO mclfamily(7) for an overview of all the documentation and the utilities in the mcl family. clm mate 12-068 8 Mar 2012 clm mate(1)