Shiny Contest Submission: Interactively view and subset phylogenetic trees

shiny-contest

#1

This shiny application allows for users to interactively view and subset phylogenetic trees by harnessing the power of the treeio and ggtree packages.

This can be useful when working with phylogenetic trees. There is software outside of R that allows users to visualize these trees but it can be clunky (and not free!) to use. This shiny app harnesses the very powerful ggtree package to make the visualization clean and easy to navigate. Once the desired tree is uploaded (There are options to upload most of the tree software output types that are provided by treeio - see here). The user has the ability to adjust the number of ancestral levels from the selected node to include in the tree. They are also able to adjust the height and width of the plot which allows for users to make the plot very large and scroll through the tree to see how different species are related.

You can find the app here: https://tbradley.shinyapps.io/tree-subset-shiny/
You can access the RStudio Cloud Project here: https://rstudio.cloud/project/165227
My github repo for the project can be found here: https://github.com/tbradley1013/tree-subset-shiny

You can find example trees to input in the data/ folder of the Cloud project. These example datasets correspond to different input options (have the input type in the name). All of these data sets are taken from (and slightly renamed to make the type more clear) the treeio package and can also be found in the treeio/extdata folder of your package install.

Here is a gif example:

I wrote a blog post about the functionality of the tree_subset function in the treeio package which also introduces the shiny app that can be found here:


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