Modernize Day 1-4 Vignettes#10
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Pull request overview
This PR updates the Day 1–4 course vignettes to use more modern R/Bioconductor tooling and plotting idioms (ggplot2-based figures, SingleCellExperiment workflows, and modern regression summaries).
Changes:
- Replaced multiple base R plots (hist/qqnorm/boxplot/scatter/volcano/p-value hist/MA) with ggplot2-based equivalents and multi-panel layouts.
- Refactored the Day 2 tissue expression workflow to store expression + metadata in a
SingleCellExperimentand usescaterplotting helpers. - Updated regression-table rendering in Day 3 to use
broom/knitrtables andgtsummaryregression summaries.
Reviewed changes
Copilot reviewed 5 out of 5 changed files in this pull request and generated 10 comments.
| File | Description |
|---|---|
| vignettes/day1_intro.Rmd | Switches several distribution/CI visuals to ggplot2 and adds a new null p-value demonstration + practical SummarizedExperiment example. |
| vignettes/day2_unsupervised.Rmd | Introduces a SingleCellExperiment-centric workflow and modern PCA/MDS/TSNE/UMAP plotting. |
| vignettes/day3_linearmodels.Rmd | Updates coefficient visualization to ggplot2 annotations and modernizes regression table output. |
| vignettes/day4_batcheffects-vis.Rmd | Replaces multiple exploratory plots with ggplot2 and patchwork-based multi-panel layouts. |
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| library(UsingR) | ||
| library(rafalib) | ||
| library(ggplot2) | ||
| library(patchwork) |
| boxplot(exec.pay, ylab="10,000s of dollars", ylim=c(0,400), main = "CEO Compensation") | ||
| ```{r bp1, echo=FALSE, fig.width=10, fig.height=4, warning=FALSE} | ||
| library(ggplot2) | ||
| library(patchwork) |
| ) | ||
| ```{r cor1, echo=FALSE, fig.width=10, fig.height=4, warning=FALSE} | ||
| library(ggplot2) | ||
| library(patchwork) |
| hist(nullpvals, ylim = c(0, 1400)) | ||
| ```{r pvalhist2, echo=FALSE, fig.height=3, fig.width=8, warning=FALSE} | ||
| library(ggplot2) | ||
| library(patchwork) |
| rafalib::mypar(1, 2) | ||
| ```{r pvalhist4, fig.height=4, fig.width=8, warning=FALSE} | ||
| library(ggplot2) | ||
| library(patchwork) |
| fit.table <- xtable::xtable(fit, label=NULL) | ||
| print(fit.table, type="html") | ||
| ```{r, echo=TRUE, message=FALSE} | ||
| gtsummary::tbl_regression(fit) |
| fit.table <- xtable::xtable(fit, label=NULL) | ||
| print(fit.table, type="html") | ||
| ```{r, echo=TRUE, message=FALSE} | ||
| gtsummary::tbl_regression(fit) |
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Copilot stopped work on behalf of
lwaldron due to an error
July 3, 2026 11:52
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This PR modernizes the vignettes for days 1-4 by moving to ggplot2, SingleCellExperiment, and modern data tables (gtsummary).