Skip to content

Commit

Permalink
🎨 update enrichmentplot example (#24)
Browse files Browse the repository at this point in the history
* 🎨 reoder example: from less to more functional enriched groups

* 🎨 try rendering plotly figure in docs correctly using figurewidget

see: https://plotly.com/python/figurewidget/

* 🐛 update nb metadata

* 🐛 increase global execution timeout to 2mins

* 🐛 exclude latest version

* 🐛 check lower version

* 🐛 FeatureWidget not available per default?

* 🎨 improve layout and one plot

* ⏪ only exclude latest gseapy version

* 🎨 typos

* 🐛 FigureWidget did not work, try Figure

* 🐛 try show method, and use basic example from plotly

Also started failing on mystnb docs: https://myst-nb.readthedocs.io/en/latest/render/interactive.html#plotly

* 🐛 try to downgrad plotly

* 🐛 fix installation

* 🎨 cleanup notebook

* 🎨 remove dependency again

* 🎨 more explanations, less

* 🎨 add explicit target and link to processing notebook

reference:
https://docs.readthedocs.com/platform/stable/guides/cross-referencing-with-sphinx.html

* 🎨 update link

* 🚧 create processing function for uniprot results

- needs to be further tested and evaluated

* 🎨 remove unused variable

* 🎨 better plots (and one typo fix)
  • Loading branch information
enryH authored Feb 21, 2025
1 parent ddfbd14 commit c1b61aa
Show file tree
Hide file tree
Showing 8 changed files with 221 additions and 143 deletions.
4 changes: 2 additions & 2 deletions docs/api_examples/Download_PRIDE_data.py
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@
# This notebook shows how `acore` can be used to download data from
# the Proteomics Identifications Database - PRIDE -
# ([ebi.ac.uk/pride/](https://www.ebi.ac.uk/pride/))
# and parse the data to be used in the analytics core.
# and parse the data to be used in the analytics core
# and quickly formated to start analyzing them with the functionality in the analytics core.
#
# > based on CKG recipe: [Download PRIDE Data](https://ckg.readthedocs.io/en/latest/notebooks/recipes/Download_PRIDE_data.html)
Expand All @@ -36,7 +36,7 @@
# %% [markdown]
# ## Parameters
# Specify the PRIDE identifier and file to be downloaded
# - and where to store intermediate files.
# and where to store intermediate files.

# %% tags=["parameters"]
pxd_id: str = "PXD008541" # PRIDE identifier
Expand Down
Loading

0 comments on commit c1b61aa

Please sign in to comment.