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lmrodriguezr / nonpareil

Estimate metagenomic coverage and sequence diversity
http://enve-omics.ce.gatech.edu/nonpareil/
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The problem with xlim #33

Closed IM-han closed 6 years ago

IM-han commented 6 years ago

When I plot a curve with the code "Nonpareil.curve.batch(File,libnames=Name,xlim = c(1e+8,1e+15))",but the xlim didnot work.　The picture is below. I want to get the x-axis bigger, so that it can show more information. The parameter xlim only work in Nonpareil.curve(), and it dosenot work in Nonpareil.curve.batch(). And I want to know what mean is the "arrow" in a picture. default

gunturus commented 6 years ago

The arrow points to the inflection point of the curve.

lmrodriguezr commented 6 years ago

Hello @IM-han

Try passing xlim explicitly as a plot option:

Nonpareil.set(File, labels=Name, plot.opts=list(xlim=c(1e+8,1e+15)))
IM-han commented 6 years ago

Thank you. I get it. How about the picture below. Dose the circle on the curve mean the same with the arrow in the picture I get ? default

lmrodriguezr commented 6 years ago

No, the circle means the actual sequencing effort and estimated average coverage of the sample. It's the equivalent to the rightmost end of the solid lines in the previous figure.

You can check out this example: http://enve-omics.ce.gatech.edu/nonpareil/results?jid=example1

Play with the radio selects (Plot model only, Plot curve only, and Plot curve and model) to see how they correspond to each other.

It's strange that this last figure doesn't include the arrows, perhaps you turned off the arrow plotting with plot.diversity=FALSE? Or maybe they happen to be hidden behind the legend box?

I'm closing this issue, but please feel free to comment again and/or reopen if you have any more questions.