Enveomics collection

A toolbox for microbial genomics and metagenomics

Table.prefScore.R

Estimate preference score of species based on occupancy in biased sample sets.

    See source code, Artistic license 2.0.

§ References

    Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

§ Usage

Table.prefScore.R --x in_file --set in_file [opts] out_file [opts]

§ Arguments

Occupancy matrix*
 --x in_file  A tab-delimited table of presence/absence (1/0) with species as rows and samples as columns.
Sample set*
 --set in_file  A list of sample names that constitute the test set, one per line.
Ignore
 --ignore in_file  A list of species to exclude from the analysis, one per line.
Significance threshold
 --signif-thr float  Absolute value of the significance threshold.
Col above
 --col-above string  Color for points significantly above zero.
Col equal
 --col-equal string  Color for points not significantly different from zero.
Col below
 --col-below string  Color for points significantly below zero.
Output preference scores*
 out_file  Output raw-text file with preference scores.
Graphical utput
 out_file  Output PDF file with preference scores plot.
Width
 float  Width of the plot in inches (7 by default).
Height
 float  Height of the plot in inches (7 by default).
* Mandatory.