Help tab gained a “Supported Drugs” catalogue: the full ~1,450-compound DepMap screen with the 44 pre-trained models marked, filterable by Pre-trained / Demo / All compounds with debounced search.
New guided walkthroughs on the Help tab (Demo and Advanced tours) with retaken, correctly-sized screenshots.
Reworked the Advanced tour steps: three input files, Seurat clustering, pre-trained vs. trained models, training output, prediction and visualisation reading order.
Improvements
README, vignettes and tutorial sections rearranged and synced with the app.
PERCEPTIONx 0.2.0
New features
Redesigned the visualization tab as a “plot gallery”: all 7 plot types visible as clickable cards, a data-readiness bar showing what is loaded, and click-to-draw (no Generate button). Parameter changes (drug / gene / ROC pair) redraw the plot automatically; hovering a card previews its description before you commit; generated-at timestamps are shown in UTC.
Seurat clustering now reports live stage progress (normalizing / variable features / PCA / clustering / UMAP / …) in the Load Demo overlay.
Demo data is more realistic and reproducible: tumor-heterogeneity mixing (responder/non-responder cells mixed 65/35 per patient) brings the ROC AUC from a perfect 1.0 to ~0.86, tighter noise-gene range sharpens the UMAP clone layout, and a fixed seed makes every Load Demo identical.
Layout widths unified across Train / Predict / Visualize (sidebar ratio 4:8); Data readiness order now groups the three user-uploaded inputs first.
annotate_clones() / prepare_data() gained an optional progress_cb and a variable_selection option (vst default; dispersion/mvp for speed).
Bug fixes
Background workers could not start in container deployments (“Failed to start the background worker … invalid connection”). Spawning now tries a ladder of progressively simpler callr configs (supervise + stderr file -> /dev/null -> inherited stdio) and reports rich diagnostics on final failure.
stdout = FALSE was rejected with EACCES in the rocker/shiny-verse container; stdout now redirects to /dev/null instead.
Removed closeAllConnections() from the Shiny session-end callback; it corrupted the process connection table and killed later spawns.
DepMap load no longer disconnects the session; demo load failures fixed.
Clearing demo data now also drops stale predictions; invalid expression files are rejected up front.
ROC curve corners (0,0) / (1,1) no longer render as a broken line (smoothed coords are densified onto a uniform FPR grid).
ROC / boxplot defaulted to the first drug on first click instead of the selected “Combination” (selectize init race); Gene Expression no longer shows “Select a gene first” on first draw.
DepMap cache is never auto-expired on disk (removed the TTL cleanup that could delete a 567 MB pre-downloaded cache); cache_ttl_hours <= 0 no longer deletes the file immediately.
Removed a stray inst/shiny/app/FALSE binary file from the repository.
Changes
Removed the on-disk TTL mechanism for the DepMap cache; memory is instead released by the master worker’s idle timeout.
