enve.recplot: Enveomics: Recruitment Plots
In enveomics.R: Various Utilities for Microbial Genomics and Metagenomics

enve.recplot

R Documentation

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.