search

nsh87 / receptormarker

Source for 'receptormarker' package for R: antibody receptor and phenotypic marker analysis
http://receptormarker.com
BSD 2-Clause "Simplified" License
4 stars 9 forks source link

Radial phylo improvements: arc size, color wheel, alternative ring annotations, labels off, distance matrix #68

Closed nsh87 closed 7 years ago

nsh87 commented 8 years ago

This PR creates a number of improvements to radial_phylo():

  1. Allows users to remove sequence labels from the phylogram by settings label=FALSE.
  2. Allows users to set a different distance matrix to use for distance tree calculations. This value gets sent to Biopython to be used on the MUSCLE alignment.
  3. Allows users to send a color wheel (a list of hex colors) to specify the colors to use for ring annotations.
  4. Adds an alternative method for ring annotations: annotate unique values from a single column. This also creates a legend at the bottom of the phylogram to indicate what values correspond to the colors.
  5. Adds a parameter and auto-calculation of arc size - the split size in the circle. This can be used to tighten up phylograms with few numbers of sequences.
    • [ ] Need to add legend for when user uses original type of ring annotations.