TODO

TODO list:

1. collapseTree source
  - X how does the collapsetree fuction work already
  - X how are mouse click selections interpreted/fed to the actual tree-collapsing part of the function?
2. metadata
  - X figure out if we need to use any specific data formats/which are most beneficial (i.e. a tibble or data.frame)
  - X decide if we want a stylesheet format (like the dummy example), or for the inputs to be provided as character vectors ( i.e. collapse = c("Rank3"), exclude = c("Helianthus", "Entamoebae") )
  - X collect lists of tree tips to collapse based on metadata
  - X get node list from list of tips to collapse
  - X prune list based on depth in tree (don't include redundant collapse commands, only supply base node where all children are going to be collapsed)
3. new functionality
  - X use splitTree function to collapse our tree
  - X select nodes to collapse based on tips
  - X collapse nodes
  - X label collapsed nodes based on shared ranks
4. integration
  - X write wrapper for all of the above
  - X with parameters for different exclusion forms (string vector vs column in metadata)
5. test code!
  - construct test set for more stringent testing
  - test with that
  - test with larger dataset (real data)
6. write documentation
  - manual page for ?metadataCollapseTree
  - toy example for users?
7. wish list...
  - specify the desired labels of the result tree (i.e want original labels, or rank5 labels, or combined tip and rank labels)
  - collapse different taxa by different ranks
  - ???