Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Changes for MVP-4632 #56

Merged
merged 2 commits into from
Nov 1, 2023

Conversation

ubyndr
Copy link
Collaborator

@ubyndr ubyndr commented Oct 27, 2023

  • Added Library Documentation link to README.md.
  • Added MissingAnalysisProcess exception to warn users to use any of the co_annotation_report method before using GraphGenerator.
  • Refactored couple of test cases for the previous changes.
  • Start nodes can already be selected with labels using node_selector. See explanations below;
def visualize_rdf_graph(
    self,
    predicate: Optional[str] = None,
    start_node: Optional[List[str]] = None,
    node_selector: Optional[Dict[str, str]] = None,
    file_path: Optional[str] = None,
    bottom_up: Optional[bool] = True,
):
node_selector: A dictionary specifying how to select a node when node URIs are not used.
    Defaults to None. The dictionary should have the following format:

    - To select by label:
        {'property': 'label', 'value': 'x label'}

    - To select by annotation:
        {'property': 'x_annotation', 'value': 'xxxx'}

    - The 'property' key represents the property that will be queried.
    - The 'value' key represents the desired property value to match.

@ubyndr ubyndr requested a review from hkir-dev October 27, 2023 15:43
@hkir-dev
Copy link
Collaborator

hkir-dev commented Oct 31, 2023

Some suggestions to improve walkthrough.ipynb

  • At cell 22, can we update gg.visualize_rdf_graph step to use the node_selector with label? Because ids are auto generated and making it hard to do copy>paste>run at this step.
  • At Cell 16 should we provide author_cell_type_list to AnndataEnrichmentAnalyzer constructor? It didn't worked without that parameter in my case.

@ubyndr ubyndr merged commit cabb406 into main Nov 1, 2023
@ubyndr ubyndr deleted the MVP-4632-pandasaurus-cxg-bug-fix-improvement-work branch November 1, 2023 13:13
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants