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labeling of exons (junctions?) #3
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I really like the idea of labelling Thinking this through, I think such a label could currently be achieved by adding something like e.g. For the junction case, I do think a Thank you for your feedback, super helpful @gpertea! |
Thank you -- using |
- Create curves for junctions ourselves using grid:::calcControlPoints. The biggest advantage of this is to plot a geom_label on the middle point of curve.
- make internal for use in geom_junction_label_repel
I've added both the exon number helper function and method for labelling junctions. For the junction label, I went for a separate label geom that inherits from One thing I was considering is whether to provide a helper function (pretty much what is used internally by Let me know if you have any additional thoughts regarding the above - thank you! |
Thank you for the detailed work on this and the documentation, the examples are great! A lot of work, really appreciated. |
- in prep for allowing shorten_gaps() to work with utrs/CDS, we need to make sure shorten_gaps() will check type column and also take user inputted type when available
For transcripts with many exons it would useful to have the option to display the exon order numbers inside the exon (or above/below when the exon height is variable or too small?).
Perhaps a dedicated boolean option to just enable/disable the automatic drawing of exon order numbers for each transcript, with another option for its placement?
A more generic solution would be mapping such exon labels to some GTF exon attribute, like
cov
orexon_number
as found in StringTie output -- maybe alabel
option can be added togeom_range()
or its aesthetics. However in many cases theexon_number
attribute is missing so a helper function could be added to generate that automatically in that case..As for labeling junctions, I suppose a labeling option could be added to
geom_junction()
to enable showing the numeric coverage values (supporting reads) for each junction, above the junction curve for top curves, or below for bottom ones.The text was updated successfully, but these errors were encountered: