Jan-Philipp Quast

Infinite values with `geom_histogram()` and `scale_y_log10()`

3

Dear package maintainer, I am trying to generate a histogram plot containing two groups with a log10 transformed y-axis. I would expect that missing values would just be ignored for...

Add "magnesium cation" ChEBI ID to GO:0016851

3

I added CHEBI:39127 (magnesium cation) to GO:0016851 ("magnesium chelatase activity). It would be great if this entry could be updated accordingly.

`fetch_uniprot()` finds a valid UniProt accession in for example: "CON_ENSEMBL:ENSBTAP00000037665", which is wrong.

Improvement to `assign_peptide_type()`

1

Make `assign_peptide_type()` recognise if the initial methionine of a protein is missing in all peptides and assign "fully-tryptic" instead of "semi-tryptic".

Add `element_blank()` for `qc_peptide_type()` x-axis title.

If the `id_nonpolymer` column is `"NA"` for `"SODIUM ION"` it is imported as `NA` (missing value) instead. In this specific case check if the `name_nonpolymer` is `"SODIUM ION"`, if yes...

"calcium ion" is not "metal cation"

2

Technically `CHEBI:39124` calcium ion should not have the outgoing ontology to `CHEBI:25213` metal cation since it is an ion and not a cation. "calcium cation" is correctly connected to "metal...

There is a missing `is_a` outgoing ontology for `CHEBI:33500` uranium cation to `CHEBI:25213` metal cation. Would be great if this could be added. Thanks!

Hi Constantin, thank you very much for the great package! I came across a bug when manually supplying values through a data frame. As you can see below, the label...

This adds the `fetch_interpro()` function. The function still needs work with the error handling and failing gracefully. This should be inspired by `fetch_uniprot()`.