enve recplot2

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Description

Produces recruitment plots provided that BlastTab.catsbj.pl has been previously executed.

Usage

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enve.recplot2(prefix, plot = TRUE, pos.breaks = 1000, id.breaks = 300, 
    id.metric = c("identity", "corrected identity", "bit score"), 
    id.summary = sum, id.cutoff = 95, threads = 2, verbose = TRUE, 
    ...)

Arguments

prefix

Path to the prefix of the BlastTab.catsbj.pl output files. At least the files .rec and .lim must exist with this prefix.

plot

Should the object be plotted?

pos.breaks

Breaks in the positions histogram. It can also be a vector of break points, and values outside the range are ignored. If zero (0), it uses the sequence breaks as defined in the .lim file, which means one bin per contig (or gene, if the mapping is agains genes).

id.breaks

Breaks in the identity histogram. It can also be a vector of break points, and values outside the range are ignored.

id.metric

Metric of identity to be used (Y-axis). Corrected identity is only supported if the original BLAST file included sequence lengths.

id.summary

Function summarizing the identity bins. Other recommended options include: 'median' to estimate the median instead of total bins, and ‘function(x) mlv(x,method=’parzen')$M' to estimate the mode.

id.cutoff

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

Number of threads to use.

verbose

Indicates if the function should report the advance.

...

Any additional parameters supported by 'plot.enve.RecPlot2'.

Value

Returns an object of class 'enve.RecPlot2'.

Author(s)

Luis M. Rodriguez-R [aut, cre]

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