Nonpareil curves

The estimation of the Redundancy is at the core of Nonpareil, but it's when those values are transformed into average coverage that they become comporable across samples, and become useful for project design and sample evaluation.

To build Nonpareil curves, you need two things. First, the Nonpareil.R file (you can find it in the utils folder of Nonpareil). Second, the .npo file (or -o value, if you used this option) generated in the estimation of Redundancy.

For the impatient

First, load the package. If you don't have it installed yet, you can open R and execute:

install.packages('Nonpareil');
library(Nonpareil);

If you did make install (Install Nonpareil), you can simply open R and execute:

library(Nonpareil);

And you can get help messages using any of:

?Nonpareil.curve
?Nonpareil.set
?Nonpareil.legend
?Nonpareil.predict

Now, you can simply execute:

Nonpareil.curve('output.npo'); # Change output.npo to the actual redundancy file.

Nonpareil.curve()

This function can generate a Nonpareil curve from a .npo file. See the documentation of this function inside R after loading the Nonpareil package:

?Nonpareil.curve

Nonpareil.set()

This function can generate a plot with several Nonpareil curves from .npo files. See the documentation of this function in R after loading the Nonpareil package:

?Nonpareil.set

Example: I find it very convenient to first prepare a table with the samples, something like:

# samples.txt
File        Name    Col
SRS063417.1.L50.npo Posterior fornix        "#FFC8C8"
SRS063287.1.L50.npo Buccal mucosa   "#FF7878"
SRS062540.1.L50.npo Tongue dorsum   "#FF0303"
SRS016335.1.L50.npo Stool   "#C8874C"
SRS015574.1.L50.npo Supragingival plaque    "#E66478"
SRS019087.1.L50.npo Anterior nares  "#DCDC82"

Note that this table is tab-delimited, because I find it easier to read, but you can use anything you like (and is supported by R). Next, you can simply type something like this in the R console:

library(Nonpareil);
samples <- read.table('samples.txt', sep='\t', header=TRUE, as.is=TRUE);
attach(samples);
nps <- Nonpareil.set(File, col=Col, labels=Name, plot.opts=list(plot.observed=FALSE));
detach(samples);
summary(nps);

To execute examples with real data included in the package, you can execute:

example(Nonpareil.curve);
example(Nonpareil.set);