enve.recplot2 {enveomics.R}

Enveomics: Recruitment Plot (2)

Description

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

Usage

enve.recplot2(
  prefix,
  plot = TRUE,
  pos.breaks = 1000,
  pos.breaks.tsv = NA,
  id.breaks = 60,
  id.free.range = FALSE,
  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). Ignored if 'pos.breaks.tsv' is passed.

pos.breaks.tsv

Path to a list of (absolute) coordinates to use as position breaks. This tab-delimited file can be produced by GFF.catsbj.pl, and it must contain at least one column: coordinates of the break positions of each position bin. If it has a second column, this is used as the name of the position bin that ends at the given coordinate (the first row is ignored). Any additional columns are currently ignored. If NA, position bins are determined by pos.breaks.

id.breaks

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

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

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]

Kenji Gerhardt [aut]