table of contents
mcx q(1) | USER COMMANDS | mcx q(1) |
NAME¶
mcxquery - compute simple graph statistics
SYNOPSIS¶
mcxquery is not in actual fact a program. This manual page documents the behaviour and options of the mcx program when invoked in mode query. The options -h, --apropos, --version, -set, --nop, -progress <num> are accessible in all mcx modes. They are described in the mcx manual page. mcxquery [-abc <fname> (specify label input)] [-imx <fname> (specify matrix input)] [-o <fname> ( output file name)] [-tab <fname> (use tab file)] [--node-attr (output node degree and weight attributes) ] [-vary-threshold <start/end/step> ( analyze graph at similarity cutoffs)] [-vary-knn <start/end/step> ( analyze graph for varying k-NN)] [-vary-ceil <start/end/step> ( analyze graph for varying ceil reductions) ] [--no-legend (do not output explanatory legend) ] [--reduce (use reduced matrix)] [--test-metric ( test whether graph distance is metric)] [--test-cycle (test whether graph contains cycles)] [-test-cycle <num> ( test cycles, report cycles)] [--vary-correlation (analyze graph at correlation cutoffs)] [--clcf (include clustering coefficient analysis) ] [--eff (include efficiency criterion)] [-div <num> (cluster size separating value) ] [--dim (report native format and dimensions)] [--values (output all arc entries/weights, unsorted) ] [--values-sorted (output all entries/weights, sorted) ] [-values-hist <nbins|start/end/nbins> (weight histogram) ] [-degrees-hist <step> (degrees histogram) ] [--output-table (output logical tab separated table without key) ] [-t <num> (number of threads to use) ] [-icl <fname> (input clustering) ] [-tf spec (apply tf-spec to input matrix) ] [-h (print synopsis, exit)] [--apropos ( print synopsis, exit)] [--version (print version, exit)]
DESCRIPTION¶
The default mcxquery output is a list of summary statistics for each node. These are its node degree, the mean, minimum, maximum and median edge weight. If supplied with a clustering, the output will additionally list the cluster size and cluster label for each node. Additionally, mcxquery can be used to analyse a graph at different similarity cutoffs or at varying parameters of edge reduction strategies such as mutual nearest neighbour reduction. Attributes supplied across different thresholds are the number of connected components, the number of singletons, and statistics (median, average, iqr) on node degrees and edge weights. Typically this is done on a graph constructed using a very permissive threshold. For example, one can create a graph from array expression data using mcxarray with a very low pearson correlation cutoff such as 0.5 Then mcxquery can be used to analyze the graph at increasingly stringent thresholds of 0.50, 0.55, 0.60 .. 0.95. Other tasks that mcxquery be used for include:
• Produce a histogram of edge weights.
• Produce a histogram of edge node degrees.
• Output all edge weights.
• Test whether the graph weight encodes a metric (for edge weights that encode distances rather than similarites).
• Test whether the graph has a cycle.
OPTIONS¶
-abc <fname> (label input)
-imx <fname> (input matrix)
-o <fname> (output file name)
-tab <fname> (use tab file)
--dim (report native format and dimensions)
--values (output all entries/weights, unsorted)
--values-sorted (output all entries/weights, sorted)
-values-hist <start/end/nbins> (output weight histogram)
-values-hist <nbins> (output weight histogram)
-degrees-hist <nbins> (degrees histogram)
--output-table (output logical tab separated table without key)
-vary-threshold <start/end/nbins> (analyze graphs at similarity cutoffs)
--vary-correlation (analyze graphs at correlation cutoffs)
defopt{--no-legend}{do not output explanatory legend}
--clcf (include clustering coefficient analysis)
--eff (include efficiency criterion)
-vary-knn <start/end/step> (analyze graphs for varying k-NN)
-vary-ceil <start/end/step> (analyze graphs for varying ceil reductions)
--reduce (use reduced matrix)
--test-cycle (test whether graph contains cycles)
-test-cycle <num> (test cycles, report cyclees)
--test-metric (test whether graph distance is metric)
-div <num> (cluster size separating value)
-tf <tf-spec> (transform input matrix values)
-t <num> (number of threads to use)
--node-attr (output node degree and weight attributes)
-icl <fname> (input clustering)
SEE ALSO¶
mcxio(5), and mclfamily(7) for an overview of all the documentation and the utilities in the mcl family.
16 May 2014 | mcx q 14-137 |