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selkamand / ggoncoplot

Easily Create Interactive Oncoplots
https://selkamand.github.io/ggoncoplot/
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Add support for grouping oncoplot by pathways #50

Closed selkamand closed 1 year ago

selkamand commented 1 year ago

Think about:

  1. how should sorting be affected.
  2. how should you chose which pathways to show first/second/third etc.
  3. What should input look like (almost certainly a 2-column dataframe: 1 with genes, 1 with pathways)
selkamand commented 1 year ago

Could be powered by facet, with labels on the left side, and free y axis scaling

selkamand commented 1 year ago

In fact, I think we should generalise this solution, and add ability to add the ability to parse a df to group genes by anything, not just pathways.

Also, after some thought:

1. how should sorting be affected Gene sorting should happen like normal. Then after that, pathway sorting will be controlled by pathway levels, which should, by default, be sorted based on the sum of samples with mutations in any member of the pathway. Would be nice to be able to define a custom order as well.

2. how should you chose which pathways to show first/second/third etc. See above

3. What should input look like (almost certainly a 2-column dataframe: 1 with genes, 1 with pathways) Exactly as above. can specify which column is which based on col_ arguments. Gene column should be named the same as the mutation dataset. Pathways could be named anything, and just be the other column