Produces recruitment plots provided that BlastTab.catsbj.pl has
been previously executed.
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,
...
)Returns an object of class enve.RecPlot2.
Path to the prefix of the BlastTab.catsbj.pl output files. At
least the files .rec and .lim must exist with this prefix.
Should the object be plotted?
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.
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.
Breaks in the identity histogram. It can also be a vector of break points, and values outside the range are ignored.
Indicates that the range should be freely set from the observed values. Otherwise, 70-100% is included in the identity histogram (default).
Metric of identity to be used (Y-axis). Corrected identity is only supported if the original BLAST file included sequence lengths.
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.
Cutoff of identity metric above which the hits are considered
in-group. The 95% identity corresponds to the expectation of
ANI<95% within species.
Number of threads to use.
Indicates if the function should report the advance.
Any additional parameters supported by plot.enve.RecPlot2.
Luis M. Rodriguez-R [aut, cre]
Kenji Gerhardt [aut]