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