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RDP AbundanceStats

Intro

This package computes Shannon and Chao diversity indices, jaccard or sorensen abundance stats and rarefaction curve. See more details on http://rdp.cme.msu.edu/tutorials/cluster/RDPtutorial_CLUST-RESULTS.html.

Setup

Usage

  • Compute Shannon and Chao1 indices

      java -cp /path/to/AbundanceStats.jar edu/msu/cme/rdp/abundstats/ShannonChao all_seq_complete.clust shannchao

  • Compute jaccard or sorensen abundance stats

      java -jar /path/toAbundanceStats.jar
  usage: Main [options] <cluster file>
  -j,--jaccard              Compute jaccard abundance stats
  -l,--lower-cutoff <arg>   Lowest cutoff in the cluster file to compute stats for
  -r,--result-dir <arg>     Directory to put the result files in (default=.)
  -R,--R-location <arg>     Triggers the R plotter subsystem, provide the path to the R command
  -s,--sorensen             Compute sorensen abundance stats
  -t,--otu-table            input file is an otu table, not rdp cluster file
  -u,--upper-cutoff <arg>   Highest cutoff in the cluster file to compute stats for

    An example command to calculate jaccard distance matrix, perform UPGMA clustering and plot dendrogram in R environment.

      java -jar /path/to/AbundanceStats.jar -jaccard -R /usr/bin/R all_seq_complete.clust

  • Calculate rarefaction curve

      java -cp /path/to/AbundanceStats.jar edu/msu/cme/rdp/rarefaction/Rarefaction all_seq_complete.clust rarefaction plot