BlastTab.recplot2.R
Produce recruitment plot objects provided that BlastTab.catsbj.pl has been previously executed.
See source code, Artistic license 2.0.
§ References
Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.
§ Requirements
§ Usage
BlastTab.recplot2.R --prefix in_file [opts] out_file [opts]
§ Arguments
- Prefix*
--prefix in_file
Path to the prefix of the BlastTab.catsbj.pl output files. At least the files .rec and .lim must exist with this prefix.- Pos breaks
--pos-breaks integer
Breaks in the positions histogram.- Pos breaks tsv
--pos-breaks-tsv in_file
File with (absolute) coordinates of breaks in the position histogram.- Id breaks
--id-breaks integer
Breaks in the identity histogram.- Id free range
--id-free-range
Indicates that the range should be freely set from the observed values. Otherwise, 70-100% is included in the identity histogram (default).- Id metric
--id-metric select
Metric of identity to be used (Y-axis). Corrected identity is only supported if the original BLAST file included sequence lengths.- Id summary
--id-summary string
Function summarizing the identity bins.- Id cutoff
--id-cutoff float
Cutoff of identity metric above which the hits are considered 'in-group'. The 95% identity corresponds to the expectation of ANI<95% within species.- Threads
--threads integer
Number of threads to use.- No verbose
--no-verbose
Indicates if the function should report the advance.- Peaks col
--peaks-col string
Color of peaks, mandatory for peak-finding (e.g., darkred).- Peaks method
--peaks-method select
Method to detect peaks.- R Object Output*
out_file
Recplo2 object that can be re-plotted using R function plot.- Graphical Output
out_file
Recruitment plot in PDF.- Width
float
Width of the plot in inches (7 by default).- Height
float
Height of the plot in inches (7 by default).