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).