enve.recplot {enveomics.R}

Enveomics: Recruitment Plots

Description

Produces recruitment plots provided that BlastTab.catsbj.pl has been previously executed. Requires the gplots library.

Usage

enve.recplot(
  prefix,
  id.min = NULL,
  id.max = NULL,
  id.binsize = NULL,
  id.splines = 0,
  id.metric = "id",
  id.summary = "sum",
  pos.min = 1,
  pos.max = NULL,
  pos.binsize = 1000,
  pos.splines = 0,
  rec.col1 = "white",
  rec.col2 = "black",
  main = NULL,
  contig.col = grey(0.85),
  ret.recplot = FALSE,
  ret.hist = FALSE,
  ret.mode = FALSE,
  id.cutoff = NULL,
  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.

id.min

Minimum identity to be considered. By default, the minimum detected identity. This value is a percentage.

id.max

Maximum identity to be considered. By default, 100%.

id.binsize

Size of the identity bins (vertical histograms). By default, 0.1 for identity metrics and 5 for bit score.

id.splines

Smoothing parameter for the splines in the identity histogram. Zero (0) for no splines. A generally good value is 1/2. If non-zero, requires the stats package.

id.metric

Metric of identity to be used (Y-axis). It can be any unambiguous prefix of:

• "identity"

• "corrected identity"

• "bit score"

id.summary

Method used to build the identity histogram (Horizontal axis of the right panel). It can be any unambiguous prefix of:

• "sum"

• "average"

• "median"

• "90% lower bound"

• "90% upper bound"

• "95% lower bound"

• "95% upper bound"

The last four options correspond to the upper and lower boundaries of the 90% and 95% empirical confidence intervals.

pos.min

Minimum (leftmost) position in the reference (concatenated) genome (in bp).

pos.max

Maximum (rightmost) position in the reference (concatenated) genome (in bp). By default: Length of the genome.

pos.binsize

Size of the position bins (horizontal histograms) in bp.

pos.splines

Smoothing parameter for the splines in the position histogram. Zero (0) for no splines. If non-zero, requires the stats package.

rec.col1

Lightest color in the recruitment plot.

rec.col2

Darkest color in the recruitment plot.

main

Title of the plot.

contig.col

Color of the Contig boundaries. Set to NA to ignore Contig boundaries.

ret.recplot

Indicates if the matrix of the recruitment plot is to be returned.

ret.hist

Ignored, for backwards compatibility.

ret.mode

Indicates if the mode of the identity is to be computed. It requires the modeest package.

id.cutoff

Minimum identity to consider an alignment as "top". By default, it is 0.95 for the identity metrics and 95% of the best scoring alignment for bit score.

verbose

Indicates if the function should report the advance.

...

Any additional graphic parameters to be passed to plot for all panels except the recruitment plot (lower-left).

Value

Returns a list with the following elements:

pos.marks

Midpoints of the position histogram.

id.matrix

Midpoints of the identity histogram.

recplot

Matrix containing the recruitment plot values (if ret.recplot=TRUE).

id.mean

Mean identity.

id.median

Median identity.

id.mode

Mode of the identity (if ret.mode=TRUE). Deprecated.

id.hist

Values of the identity histogram (if ret.hist=TRUE).

pos.hist.low

Values of the position histogram (depth) with "low" identity (i.e., below id.cutoff) (if ret.hist=TRUE).

pos.hist.top

Values of the position histogram (depth) with "top" identity (i.e., above id.cutoff) (if ret.hist=TRUE).

id.max

Value of id.max. This is returned because id.max=NULL may vary.

id.cutoff

Value of id.cutoff. This is returned because id.cutoff=NULL may vary.

seqdepth.mean.top

Average sequencing depth with identity above id.cutoff.

seqdepth.mean.low

Average sequencing depth with identity below id.cutoff.

seqdepth.mean.all

Average sequencing depth without identity filtering.

seqdepth.median.top

Median sequencing depth with identity above id.cutoff.

seqdepth.median.low

Median sequencing depth with identity below id.cutoff.

seqdepth.median.all

Median sequencing depth without identity filtering.

id.metric

Full name of the used identity metric.

id.summary

Full name of the summary method used to build the identity plot.

Author(s)

Luis M. Rodriguez-R [aut, cre]