enve.recplot2 | R Documentation |
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,
...
)
prefix |
Path to the prefix of the |
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 |
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: |
id.cutoff |
Cutoff of identity metric above which the hits are considered
|
threads |
Number of threads to use. |
verbose |
Indicates if the function should report the advance. |
... |
Any additional parameters supported by |
Returns an object of class enve.RecPlot2
.
Luis M. Rodriguez-R [aut, cre]
Kenji Gerhardt [aut]
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.