Enveomics collection

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

• R.
• R package optparse.
• R package enveomics.R.

§ 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).

* Mandatory.