Heatmap GFC export & PNG companions, notebook rendering, LLM model listing, Docker 1.98#4
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Heatmap GFC export & PNG companions, notebook rendering, LLM model listing, Docker 1.98#4Ulas-lab wants to merge 10 commits into
Ulas-lab wants to merge 10 commits into
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Route widget display through the htmlwidget print/viewer path so RStudio's notebook viewer renders widgets inline below the chunk. The previous repr::repr_html + cat path emitted raw HTML text in RStudio notebooks; it is now strictly opt-in (hcocena.htmlwidget_display = "inline" or options(hcocena.htmlwidget_emit_html = TRUE)) for Jupyter/IRkernel front-ends. Knitting to HTML still uses knit_print. Co-Authored-By: Claude Opus 4.8 <[email protected]>
Add shared helpers (.hc_module_label_fit_pt, .hc_module_label_box_annotation, .hc_module_label_text_width_cm, .hc_module_label_effective_fontsize, .hc_cluster_heatmap_cell_size_mm) that pick a single safe font size fitting every module label into its box (width and height bounded). Apply the guard consistently in the main cluster heatmap, functional enrichment (incl. combined all-DB headers), the Gemini/LLM module-function plot, and upstream inference. Co-Authored-By: Claude Opus 4.8 <[email protected]>
scripts/run_realdata_regression.R drives integration, clustering, module heatmaps, module splitting, enrichment, and a module-label font probe on real STAR-protocol data, exporting golden-master CSV/JSON artifacts plus a visual_check_report PDF. A testthat wrapper runs it only when HCOCENA_RUN_REALDATA=true; README documents usage and .gitignore excludes the generated output/reference dirs. Co-Authored-By: Claude Opus 4.8 <[email protected]>
…ndering Commit 4bc5122 called print.htmlwidget() directly via getFromNamespace, which bypasses the print-generic hook RStudio uses to render widgets inline in notebook chunks. As a result hc_plot_cutoffs(interactive=TRUE) opened the cutoff plots in the Viewer pane instead of below the chunk. Dispatch through the generic (print(x)) like a bare print(widget); this renders inline even when called from inside a function. The regression test now guards the dispatch at the source level. Co-Authored-By: Claude Opus 4.8 <[email protected]>
Heatmap:
- Export Module_GFC_Means.xlsx with the mean GFC per module and group
(the values behind the heatmap cells); also stored in satellite_outputs.
- Fix AnnotationFunction var_import so the module-label sizing helper
resolves at draw time instead of erroring ("function not found").
Plot exports:
- Add .hc_ggsave_pdf_png() and route longitudinal / PCA / UMAP / hub-gene
network plots through it so each PDF gets a matching 300-dpi PNG.
- Enable inline notebook display for multi-page and TF module exports.
Other (branch WIP folded in):
- hc_utils: ggplot2/ggrepel hub-gene network visualization.
- LLM: add and export hc_list_llm_models(); Claude provider listing.
- Add ggrepel to Suggests; update docker satellite workflow notebook.
Co-Authored-By: Claude Opus 4.8 <[email protected]>
Published therealtomek/hcocena:1.98 and :latest with the heatmap GFC-means export, PNG companions, var_import draw fix, and LLM model-listing. Co-Authored-By: Claude Opus 4.8 <[email protected]>
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| #' hc_list_llm_models("vllm", base_url = "http://my-server:8000/v1") | ||
| #' } | ||
| #' @export | ||
| hc_list_llm_models <- function(provider = "all", |
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When this package is checked or installed from the committed source, this newly exported function has no corresponding man/hc_list_llm_models.Rd, and the existing man/hc_module_function_llm.Rd also does not include the new provider/base_url arguments. That makes R CMD check report documentation/code mismatches and leaves users without help pages for the public API, so the roxygen-generated Rd files need to be committed with this change.
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Summary
Brings the latest heatmap, notebook-rendering, LLM, and Docker work from
codex/heatmap-column-gaps-docker-1.97intodevel(7 commits, 24 files).Heatmap
Module_GFC_Means.xlsxwith the mean GFC per module and group (the values behind the heatmap cells); also stored insatellite_outputs.AnnotationFunctionvar_importso the module-label sizing helper resolves at draw time instead of erroring ("function not found").Plot exports
.hc_ggsave_pdf_png()(heatmap + enrichment already did).Notebook rendering
LLM
hc_list_llm_models(); Claude/Anthropic provider listing; addggrepelto Suggests.Docker
therealtomek/hcocena:1.98+latest; moved1.97to the older reproducible tags.Tests
Verification
hc_list_llm_modelspresent.🤖 Generated with Claude Code