Nonpareil.set: Generates a collection of Nonpareil curves (a 'Nonpareil.Set'...

Description Usage Arguments Value Examples

View source: R/Nonpareil.R

Description

Generates a collection of Nonpareil curves (a Nonpareil.Set object) and (optionally) plots all of them in a single canvas.

Usage

1
2
Nonpareil.set(files, col = NA, labels = NA, plot = TRUE,
  plot.opts = list(), ...)

Arguments

files

Vector with the paths to the .npo files.

col

Color of the curves (vector). If not passed, values are randomly assigned. Values are recycled.

labels

Labels of the curves (vector). If not passed, values are determined by the filename. Values are recycled.

plot

If TRUE, it generates the Nonpareil curve plots.

plot.opts

Any parameters accepted by plot.Nonpareil.Set as a list.

...

Any additional parameters accepted by Nonpareil.curve.

Value

Returns invisibly a Nonpareil.Set object.

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
# Generate a Nonpareil plot with multiple curves
files <- system.file("extdata",
      c("HumanGut.npo","LakeLanier.npo","IowaSoil.npo"),
      package="Nonpareil")
col <- c("orange","darkcyan","firebrick4")
nps <- Nonpareil.set(files, col=col,
      plot.opts=list(plot.observed=FALSE, model.lwd=2))

# Show the estimated values
print(nps)

# Show current coverage (as %)
summary(nps)[,"C"]*100

# Extract Nd diversity index
summary(nps)[,"diversity"]

# Extract sequencing effort for nearly complete coverage (in Gbp)
summary(nps)[,"LRstar"]/1e9

# Predict coverage for a sequencing effort of 10Gbp
sapply(nps$np.curves, predict, 10e9)

Example output

===[ Nonpareil.Set ]===================================
Collection of 3 Nonpareil curves.
             kappa         C          LR    modelR       LRstar diversity
HumanGut   0.79021 0.8063516   323066770 0.9986240   2622136382  17.26038
LakeLanier 0.65906 0.6830866  1167543428 0.9986215  20529561329  19.21348
IowaSoil   0.52751 0.5572956 14558899784 0.9996735 662396292322  22.79596
-------------------------------------------------------
call: Nonpareil.set files col list(plot.observed = FALSE, model.lwd = 2) 
-------------------------------------------------------
  HumanGut LakeLanier   IowaSoil 
  80.63516   68.30866   55.72956 
  HumanGut LakeLanier   IowaSoil 
  17.26038   19.21348   22.79596 
  HumanGut LakeLanier   IowaSoil 
  2.622136  20.529561 662.396292 
[1] 0.9831304 0.9171014 0.5093043

Nonpareil documentation built on Jan. 29, 2022, 1:08 a.m.