Inclusion and exclusion criteria used by dotplot
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Assessment
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Newbie friendliness
- 25/100
- Issue type
- Bug
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- r
- Domain
- data-visualization
Research direction
Start by comparing the pathways returned by enrichKEGG with those rendered by dotplot, using the issue's screenshots and cutoff values as the reproduction context. Trace how significant results are selected for plotting and document which inclusion or exclusion rule accounts for the difference; done means the behavior is explained and, if it is a bug, covered by an appropriate regression check.
Written by the indexing model from the issue text.
Description
Hi,
I encountered an issue where some pathways that were passed the significant cutoffs (adjusted p<0.05 and qvalue<0.2) were not included in the dotplot. Below includes the dotplot and the top pathways returned by function enrichKEGG. Any inputs on how to address this issue are greatly appreciated. Thank you!
- Dominant language
- R
- Stars
- 260
- Forks
- 75
- PR merge metrics
- No merged PRs in 30d
Contributor guide
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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.
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- Open a pull request that references the issue number.
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