gather 10 use-cases

[arlin]

When 5 of us met Oct 3, we decided to each get 2 use-cases, such as a figure from a paper. The use-case will exemplify the kinds of tree-associated information that needs to be renderable and interoperable. I created a doc for this here:

https://github.com/OpenTreeOfLife/phylostylotastic/blob/master/analysis/use_cases1.md

[nfranz]

Hi all: Sorry if I don't get all the context. Are weevils an option?

"Broad-noses" http://taxonbytes.org/pdf/Franz2012-PhylogeneticReassessmentExophthalmus.pdf (just characters; oh, and Bremer support!! ;o) ) http://biorxiv.org/content/early/2016/05/17/053611 (biogeography)

"Belids" https://docs.google.com/document/d/1aGsuqmcrQzPx9Xd2pzwcVmqXIhQoQ9J-bu9Kw_r7K0A/edit?usp=sharing (host plants..)

Cheers, Nico

On Tue, Oct 4, 2016 at 10:17 AM, Arlin Stoltzfus notifications@github.com wrote:

When 5 of us met Oct 3, we decided to each get 2 use-cases, such as a figure from a paper. The use-case will exemplify the kinds of tree-associated information that needs to be renderable and interoperable.

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[arlin]

Nico, the context is that some of us (including Daisie and Jim) are kinda taking over this repo to turn the project into a slightly broader direction. We want to identify the kinds of information that people add to trees and (1) develop a way to serialize that (i.e., put it in a file according to some standard), (2) decide on conventions for rendering annotations graphically, and then (3) have a hackathon and challenge tree-viz programmers to support this new scheme. The original Phylostylotastic stylesheets are one way to serialize annotations to be rendered.

So, your examples are appropriate in the sense that paper 1 has a tree that shows 2 different kinds of support values on internal branches, and it has brackets on clades. The second tree shows branches annotated with character-state changes. These are features that are widely used by researchers when they present tree-based visualizations.

[arlin]

so, @nfranz, feel free to add those examples to the use-case doc mentioned above, following the pattern for the first example.

[jhcepas]

Some very common features used for species tree visualization:

• Vertical labels
• Branch length calibration rulers
• node images and silhouttes

http://www.nature.com/nature/journal/v526/n7574/fig_tab/nature15697_F1.html

• Silhouettes
• Node background
• branch length rulers
• Notes on nodes

http://www.nature.com/articles/srep20252/figures/2

• backgrounds
• vertical label bands

http://www.sciencedirect.com/science/article/pii/S1055790313000298#f0005

• collapsed nodes
• aligned data matrices http://www.nature.com/nature/journal/v504/n7479/fig_tab/nature12779_F2.html
• large trees summarized (e.g. metagenomics)
• circular tree representation
• Bars in terminal nodes

http://www.nytimes.com/interactive/2012/06/19/science/0619-microbiome.html?ref=science&_r=0

[arlin]

@jhcepas, can you put these example in analysis/use_cases1.md? then we can close this issue.

[jhcepas]

@arlin I don't have write access to the repo. Do you want a PR?