mcxq is not in actual fact a program. This manual page documents the behaviour and options of the mcx program when invoked in mode q. The options -h, --apropos, --version, -set, --nop, -progress <num> are accessible in all mcx modes. They are described in the mcx manual page.
mcxquery [-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,scale> (analyze graph at similarity cutoffs)] [-vary-knn <start,end,step,scale> (analyze graph for varying k-NN)] [-report-scale <num> (edge weight/threshold scaling)] [--knn-reduce (use reduced matrix)] [--test-cycle (test whether graph contains cycles)] [-test-cycle <num> (test cycles, report cyclees)] [--vary-correlation (analyze graph at correlation cutoffs)] [--clcf (include clustering coefficient analysis)] [-div <num> (cluster size separating value)] [--dim (report native format and dimensions)] [-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)]
The main use of mcxquery is to analyze a graph at different similarity cutoffs. 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 0.2 or 0.3. Then mcxquery can be used to analyze the graph at increasingly stringent thresholds of 0.25, 0.30, 0.35 .. 0.95. Attributes supplied across different thresholds are the number of connected components, the number of singletons, adn statistics (median, average, iqr) on node degrees and edge weights.
2m 2m -imx <fname> (input matrix)
The file name for input that is in mcl native matrix format.
2m 2m -o <fname> (output file name)
Set the name of the file where output should be written to.
2m 2m -tab <fname> (use tab file)
This option causes the output to be printed with the labels found in the tab file.
2m 2m --dim (report native format and dimensions)
This will report the matrix format (either interchange or binary) and the matrix dimensions. For a graph the two reported dimensions should be equal.
2m 2m -vary-threshold <start,end,step,scale> (analyze graphs at similarity cutoffs)
All of start, end, step and scale must be integer numbers. From these a list of threshold is constructed, starting from start / scale, (start + step) / scale, (start + 2 step) / scale, and so on until a value larger than or equal to end / scale is reached.
2m 2m --vary-correlation (analyze graphs at correlation cutoffs)
This instructs mcxquery to use a threshold list suitable for use with graphs in which the edge weight similarities are correlations. The list starts at 0.2 and ends at 0.95 using increments of 0.05. If a different start or increment is required it can be achieved by using the -vary-threshold option. For example, a start of 0.10 and an increment of 0.02 are obtained by issuing -vary-threshold 10,100,2,100.
2m 2m --clcf (include clustering coefficient analysis)
This option causes the global clustering coefficient to be computed for the analysis of thresholded graphs with --vary-correlation and -vary-threshold. For large graphs this may be time-consuming.
2m 2m -vary-knn <start,end,step,scale> (analyze graphs for varying k-NN)
2m 2m --knn-reduce (use reduced matrix)
This analyses a graph as it is subjected to varying k-NN (k mutual nearest neighbours) selection steps. The analyses starts at the end argument, and progresses towards the start argument using decrements of size step. By default the reduction is always computed relative to the start matrix, i.e. the input matrix after -tf transformations have optionally been applied. Specifying --knn-reduce causes this to change so that each new reduction is calculated relative to the reduction just computed.
For graphs with ties among edge weights it may be useful to use -tf '#tug()'. This will add small perturbations to the edge weights and have the effect of breaking ties. By default perturbations are computed using the cosine between the vectors of neighbours of the two nodes incident to an edge. This can be changed to a random perturbation with -tf '#rug()'.
2m 2m --test-cycle (test whether graph contains cycles)
2m 2m -test-cycle <num> (test cycles, report cyclees)
Test whether the input graph contains cycles. With the second option nodes that are part of a cycle are output, up to a maximum of <num> nodes. Use <num>=-1 to output all such nodes.
2m 2m -report-scale <num> (edge weight / threshold scaling)
The edge weights mean, average, and inter-quartile range, as well as the different threshold steps are all rescaled in the reported output to avoid printing of fractional part. If -vary-threshold was supplied then scaling factor specified in the argument is used. With --vary-correlation a scaling factor of 100 is used. Either can be overridden by using the present option.
2m 2m -div <num> (cluster size separating value)
When analyzing graphs at different thresholds with one of the options above, mcxquery reports the percentage of nodes contained in clusters not exceeding a specified size, by default 3. This number can be changed using the -div option.
2m 2m -tf <tf-spec> (transform input matrix values)
Transform the input matrix values according to the syntax described in mcxio(5).
2m 2m -t <num> (number of threads to use)
This has an effect only when using the -vary-knn option, and is only useful on multi-CPU machines.
2m 2m --node-attr (output node degree and weight attributes)
Output is in the form of a tab separated file. The option -icl can be used in conjuction.
2m 2m -icl <fname> (input clustering)
Output for each node the size of the cluster it is in. This option can be used in conjunction with --node-attr.
mcxio(5), and mclfamily(7) for an overview of all the documentation and the utilities in the mcl family.