metacoder

metacoder copied to clipboard

This would be used on the newick format (https://en.wikipedia.org/wiki/Newick_format) or something like HTML.

zachary-foster

@grunwald suggested adding a tree map visualization as seen in figure two in the link below: http://science.sciencemag.org/content/348/6237/1261605.figures-only

zachary-foster

This would require abstracting `primersearch` to use more than one program. Perhaps a new function named `pcr` would be best. http://pprospector.sourceforge.net/index.html

zachary-foster

In silico PCR relies on the primer sites being represented in the sequences used. Searching for sequences to use that are produced by PCR do not contain the sites of...

zachary-foster

For example, when mapping rank to color, only integers should appear on the legend, since a a rank of 1.5 does not make sense.

zachary-foster

This option should be a number, 1 by default, that determines: - How much effort is put into vertex size optimization (slow for large graphs currently) - How much effort...

zachary-foster

Add function to read fasta subset

1

Big fasta files are common. I just ran into one that would require 14GB of RAM to read into R using `ape::read.dna`. I need a way to read into subsets...

zachary-foster

Currently, the legends are designed for quantitative data, even though it is possible to plot categorical data. It would be nice to have a legend type for categorical data when...

zachary-foster

These could be added next to or in place of vertices http://phylopic.org/ https://github.com/sckott/rphylopic

zachary-foster

Each vertex could be a pie graph and each edge split into bars.

zachary-foster