Closed rdmorin closed 1 year ago
(This will also be addressed in a PR I am working on)
Since this is still open I thought it worth mentioning that some of the documentation is not very clear. Reading the docs for this function actually doesn't tell me what it's doing.
fancy_alignment_plot Description Visualize (stacked barplot) genomic read-subsets across a selection of samples.
I also found another few functions with the formatting still messed up. Can you check them all please?
fancy_cnbar fancy_ideogram fancy_multisamp_ideogram
Yes, thanks!
It seems like it's an issue for almost every GAMBLR function right now. Instead of the brief description, the entire description is recycled for both the brief (huge font) and detailed function description.
For an example of how MAFtools documentation handles this check out the first function here:
https://github.com/PoisonAlien/maftools/blob/master/R/oncoplot.R
Yes, I am aware that pretty much every function description needs to be updated in order for us to close this issue. I think It's been a rather low priority, but I will see to it that this gets taken care of in my upcoming PR
It looks like the description is being interpreted as the title for some functions because there is not a separate title line in the documentation. I've fixed this for a few functions but I'm sure it's a problem elsewhere. Here's one I fixed. Originally it had all the text on the first line, which caused ROxygen to use that as the title and the description, which cluttered the docs page due to the font size and duplication. Be sure all functions either have a sufficiently brief title that this isn't a concern OR (ideally) all have both a title and description, separated by an empty line.