Hallmark dotplot: padj clip is dead code
Nobody has claimed this yet.
Assessment
- Difficulty
- 1/5
- Estimated time
- Under an hour
- Newbie friendliness
- 88/100
- Issue type
- Bug
- Clarity
- Clearly specified
- Activity status
- Active
- Tech stack
- jupyter-notebook, python
- Domain
- data-visualization
Research direction
Open bulk/rna.ipynb and inspect the Hallmark dotplot cell alongside the PROGENy cell, focusing on how the clipped adjusted p-value is assigned and then used. Done means the Hallmark plot uses the clipped value rather than the raw p-value; rerun the cell or notebook to verify the output.
Written by the indexing model from the issue text.
Description
In bulk/rna.ipynb, the Hallmark dotplot cell does:
hm_padj.melt(value_name="pvalue")
.assign(padj=lambda x: x["pvalue"].clip(2.22e-16, 1))
.assign(padj=lambda x: np.log10(x["pvalue"]))
so the clip on the first line has no effect and the plotted dot size is log10(raw p-value).
In contrast the PROGENy correctly updates the padj column.
- Dominant language
- Jupyter Notebook
- Stars
- 0
- Forks
- 0
- PR merge metrics
- No merged PRs in 30d
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Similar issues
-
Difficulty 2/5 1-3 hours Newbie friendliness 88/100
-
scope: charts status: waiting for maintainer
Difficulty 2/5 1-3 hours Newbie friendliness 88/100
-
chore P3 plotly-internal size: 3 task
Difficulty 2/5 1-3 hours Newbie friendliness 77/100
-
Urgent request: Due to vulnerabilities move to API version 12.6.1 (12.6.2 eventually) or 13.1.1 Open
Difficulty 2/5 1-3 hours Newbie friendliness 65/100
jbkunst/highcharter#849 ·
-
Difficulty 2/5 1-3 hours Newbie friendliness 68/100
equinor/energyvision#4027 ·