announce date / release schedule

[timelyportfolio]

What is your timeline for release? I would love to feature this on http://buildingwidgets.com/blog, but don't want to prematurely announce.

[sdwfrost]

Dear @timelyportfolio

The hackathon is over, so I don't have any dedicated time to this - I spent a bit of Friday making sure that the package passed R CMD CHECK (which it does). There are a few things that need to be fixed, and a few improvements before I'd be happy with releasing.

1. The major bug right now is in selections (look at Sergei's standalone widget in inst/standalone); the main utility of the widget is the ability to tag nodes with labels, which are inserted into the Newick string. However, as some tags would break the Newick string, there is some validation code used. To try to understand (and hence later enhance) the code, I've worked through the event handlers, but there's a bug such that one can't add multiple tags or change the default 'Foreground' one.
2. The dashboard is a bit ugly; the widget is bundled with Bootstrap, so I just need to add in a grid component.
3. I added support for saving the (tagged) Newick tree to file, and an exit button (which I should make conditional on Shiny), which if run in a Shiny app, exits to the R console. It prints out the tagged tree (using Shiny.onInputChange), but I haven't worked out how to return as e.g. a Newick string that could be parsed back into ape.

There are some additional enhancements that I'd like to make, to improve support for large trees e.g. using something like Magnifier.js, and/or D3's fisheye/Cartesian distortion. These aren't essential, and someone may pick these up before I do if attention is drawn with a blog post.

[sdwfrost]

PS. Oliver Ratmann @olli0601 was working on a feature to annotate the labels of the tree e.g. with sparklines, and given the presence of phylowidget.org, we probably need to change the name too.

[olli0601]

Hi Simon - thanks.
I d be keen to continue working on the label annotation, but need help with D3 and phylotree.js. Happy to share the bits that I got working if there is interest:

• cast data.frame with label annotation into D3 friendly format
• annotate phylotree.js nodes with additional information

TODO:

• plot the areas. Sparklines don t support an x arguments, so I was aiming to subclass the area function.

Ultimately, I was aiming to achieve this (which I have in R but becomes very quickly very cluttered because a lot of different information is available):

olli

[sdwfrost]

Dear @olli0601 , please submit a pull request when you're ready! The more development, the better...

[liamxg]

@olli0601 what is your figure meaning here?

[liamxg]

Hi Simon - thanks. I d be keen to continue working on the label annotation, but need help with D3 and phylotree.js. Happy to share the bits that I got working if there is interest:

• cast data.frame with label annotation into D3 friendly format
• annotate phylotree.js nodes with additional information

TODO:

• plot the areas. Sparklines don t support an x arguments, so I was aiming to subclass the area function.

Ultimately, I was aiming to achieve this (which I have in R but becomes very quickly very cluttered because a lot of different information is available):

olli

any code to plot the figure? @olli0601