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Pull request overview
Updates the CFReT-Circ analysis plotting outputs by refreshing PCA/UMAP visual styling, adding a shuffled negative-control comparison for feature effect-size vs significance plots, and introducing a new compound score scatter plot.
Changes:
- Updated PCA/UMAP plotting script styling (larger fonts, updated facet labels) and added an “all-features” UMAP contour panel.
- Added new R plotting scripts for (a) feature effect size vs statistical significance with a shuffled control and (b) compound Buscar score scatter plot.
- Updated the R conda environment to include
r-ggsideand trimmed explicit Python dependencies.
Reviewed changes
Copilot reviewed 8 out of 21 changed files in this pull request and generated 9 comments.
Show a summary per file
| File | Description |
|---|---|
r_buscar_env.yaml |
Adds r-ggside; removes explicit Python runtime/deps from the conda env used for plotting/notebooks. |
notebooks/2.cfret-analysis/plots/nbconverted/1.on-and-off-pca-and-umap-plots.r |
Increases font sizes, updates signature labels, adds “all-features” UMAP contour faceting, and adjusts contour plot layout/export. |
notebooks/2.cfret-analysis/plots/nbconverted/3.cfret-signature-effect-size-vs-sig-plot.r |
New plot script to compare non-shuffled vs shuffled feature significance/effect size with side densities. |
notebooks/2.cfret-analysis/plots/nbconverted/4.cfret-compound-scores-plot.r |
New compound-score scatter plot with quadrant shading and repelled labels. |
notebooks/2.cfret-analysis/nbconverted/5.plot-buscar-compound-scores.ipynb |
Adds an (currently empty) R-kernel notebook placeholder. |
notebooks/2.cfret-analysis/4.assess-signature-significance.ipynb |
Refactors KS+FDR computation into a function and adds a shuffled-feature negative control export. |
notebooks/2.cfret-analysis/3.generate-pca-umap-components.ipynb |
Minor notebook output/metadata adjustments. |
.pre-commit-config.yaml |
Bumps toml-sort pre-commit hook version. |
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notebooks/2.cfret-analysis/plots/nbconverted/1.on-and-off-pca-and-umap-plots.r
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notebooks/2.cfret-analysis/nbconverted/5.plot-buscar-compound-scores.ipynb
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notebooks/2.cfret-analysis/plots/nbconverted/1.on-and-off-pca-and-umap-plots.r
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notebooks/2.cfret-analysis/plots/nbconverted/4.cfret-compound-scores-plot.r
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wli51
approved these changes
Mar 25, 2026
notebooks/2.cfret-analysis/nbconverted/5.plot-buscar-compound-scores.ipynb
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notebooks/2.cfret-analysis/plots/figures/cfret_signature_significance_plots.png
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notebooks/2.cfret-analysis/plots/figures/umap_kde_contour_by_treatment.gif
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…and-umap-plots.r Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
…-effect-size-vs-sig-plot.r Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
…and-umap-plots.r Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
…scores-plot.r Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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Thanks for the review, now merging @wli51 |
axiomcura
added a commit
to axiomcura/buscar
that referenced
this pull request
Mar 31, 2026
* updated all plots * updated plots * name changes on axis update * update * Update notebooks/2.cfret-analysis/plots/nbconverted/1.on-and-off-pca-and-umap-plots.r Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update notebooks/2.cfret-analysis/plots/nbconverted/3.cfret-signature-effect-size-vs-sig-plot.r Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update notebooks/2.cfret-analysis/plots/nbconverted/1.on-and-off-pca-and-umap-plots.r Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update notebooks/2.cfret-analysis/plots/nbconverted/4.cfret-compound-scores-plot.r Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update r_buscar_env.yaml Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * updated plots and comments * update --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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This update the plots for the CFReT-Circ results