plotly / plotly/plotly.R

ggtree support

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Description


Hello everyone. I wanted to plot a phylogeny tree thanks to ggtree R package. Yet, I have too many species (around 1000) and the graph is unreadable. Thus, I wanted to convert the plot into plotly format to be able to zoom in. But I got this error message (see below).

Thank you for your help !

tree = read.tree("ressources/phylogeny_tree.tree")
p <- ggtree(tree, layout = "circular") + 
  geom_tiplab(size = 2) + 
  theme_tree2()  
ggplotly(p)
5: In geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]) :
  geom_GeomTextGGtree() has yet to be implemented in plotly.
  If you'd like to see this geom implemented,
  Please open an issue with your example code at
  https://github.com/ropensci/plotly/issues
6: In geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]) :
  geom_GeomTextGGtree() has yet to be implemented in plotly.
  If you'd like to see this geom implemented,
  Please open an issue with your example code at
  https://github.com/ropensci/plotly/issues

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the supplied R example and the ggplotly() entry point, then trace the geom2trace.default() warning for geom_GeomTextGGtree. Done means the ggtree plot converts to Plotly without the unimplemented-geom warning and remains zoomable.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
data-visualization
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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