Fix bugs and reduce technical debt#1
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psychemistz wants to merge 18 commits intodata2intelligence:mainfrom
Open
Fix bugs and reduce technical debt#1psychemistz wants to merge 18 commits intodata2intelligence:mainfrom
psychemistz wants to merge 18 commits intodata2intelligence:mainfrom
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- Add 3-tab dataset loading: Upload Object, Space Ranger zip, Demo (Visium HCC) - Space Ranger zip upload: extract, find spatial/ dir, call create.SpaCET.object.10X() - Demo button: loads bundled Visium_HCC from inst/extdata/ - Run SecAct Inference button: calls SecAct.activity.inference.ST() on loaded data - hasSecActResults reactive flag controls inference panel visibility - Refactored load paths to share finish_load() helper
- Add on.exit() cleanup for Space Ranger zip extraction temp directory - Add missing return() after unrecognized object type error in load path 1 - Remove unused file_name variable - Extract swap_activity_matrix() to utils_viz.R (was inline in renderPlot) - Remove redundant WHAT comments in inference section
- Fix crash in sweep_sparse (x@j → m@j for non-dgCMatrix sparse matrices) - Fix undefined my_cols variable in CCC.circle and CCC.sankey (→ colors_cellType) - Fix coutourBins typo in signaling velocity parameter - Extract 8 helper functions to eliminate code duplication (~160 lines removed) - Replace 14 library() calls with :: notation and @import ggplot2 - Replace ~12 class() checks with inherits() per R CMD check guidelines - Add RANN to DESCRIPTION Imports - Remove tracked .DS_Store files and add to .gitignore - Remove dead code (commented-out hello(), color scales, score lines) - Remove unused GSL_CFLAGS/GSL_LIBS from Makevars
- Add stop() in extract_ccc_data for unrecognized input class - Replace deprecated row.names() with rownames() in activity.R - Pre-allocate numeric vectors in compute_spatial_correlation instead of growing a data.frame row-by-row
- Fix q() that kills R session on low death rate (→ stop()) - Fix hardcoded column 3 in signaling.pattern.gene (→ column n) - Fix length(death_rate) check (always 1; use death_rate directly) - Remove unused patchwork and networkD3 from Imports - Remove unused gsl_cdf.h include - Remove commented-out sprintf line
Prevents R from dropping matrix to vector when only one secreted protein matches a pattern, which would crash the subsequent column indexing.
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Summary
sweep_sparse(wrong variablex→m), undefinedmy_colsin CCC.circle/CCC.sankey,coutourBinstypolibrary()calls with::/@import, replaceclass()checks withinherits(), add missing RANN to Imports.DS_Storefiles, dead code, unused Makevars variablesTest plan
R CMD checkpasses without errors or warningsSecAct.activity.inference()produces identical results on test dataSecAct.CCC.circle()andSecAct.CCC.sankey()work with sender/receiver filters (previously crashed due tomy_colsbug)contourBinsparameter