Assay selection and Custom Upload update

.gitattributes

@@ -0,0 +1,4 @@
+* text=auto
+*.r text eol=lf
+*.R text eol=lf
+*.RDS filter=lfs diff=lfs merge=lfs -text

.github/workflows/shinytest2.yml

@@ -0,0 +1,44 @@
+on:
+  pull_request:
+    branches: [main, master, drug_signature_update]
+
+name: shinytest2
+
+jobs:
+  shinytest2:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          lfs: true
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::shinytest2
+          needs: shinytest2
+
+      - uses: browser-actions/setup-chrome@latest
+        with:
+          chrome-version: stable
+
+      - name: Install scFOCAL package
+        run: R CMD INSTALL --no-multiarch .
+
+      - name: Verify scFOCAL installed
+        shell: Rscript {0}
+        run: |
+          path <- system.file("shiny", package = "scFOCAL")
+          if (!nzchar(path)) stop("scFOCAL not installed: system.file() returned ''")
+          cat("scFOCAL shiny dir:", path, "\n")
+
+      - name: Run shinytest2 tests
+        shell: Rscript {0}
+        run: |
+          shinytest2::test_app("inst/shiny")

CLAUDE.md

@@ -0,0 +1,69 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Build & Test Commands
+
+```r
+# Rebuild package after any change to inst/shiny/ or R/
+devtools::install()          # or Build → Clean and Rebuild in RStudio
+
+# Launch app manually
+scFOCAL::runscFOCAL()
+
+# Run all shinytest2 tests
+shinytest2::test_app("inst/shiny")
+
+# Run a single test file
+testthat::test_file("inst/shiny/tests/testthat/test-upload.R")
+testthat::test_file("inst/shiny/tests/testthat/test-edge-cases.R")
+```
+
+**Critical**: Tests run against the *installed* package via `system.file("shiny", package = "scFOCAL")`. Always do a Clean and Rebuild before running tests after editing anything in `inst/shiny/` or `R/`.
+
+## Architecture
+
+**Entry point**: `R/runApp.R` — `runscFOCAL()` calls `shiny::shinyAppDir(system.file('shiny', package = "scFOCAL"))`.
+
+The Shiny app lives in `inst/shiny/server.R` + `inst/shiny/ui.R`.
+
+### Key server.R reactives
+
+| Reactive | Purpose |
+|---|---|
+| `rdsSeurat()` | Loads uploaded Seurat RDS; handles Seurat v5 layer detection |
+| `seuratLoaded` | Boolean output; used by conditional panels and tests as upload health-check |
+| `assay_to_use()` | Selects RNA vs RNA_ortho assay; guards with `req(input$seurobjRDS)` |
+| `drugSignatures()` | Accepts custom drugs×genes CSV; auto-detects orientation via gene-name overlap; falls back to built-in LINCS |
+| `corrMatUpload()` | Reads uploaded drugs×cells correlation matrix CSV |
+| `LINCS.ResponseSigs()` / `L1000_genes` | Built-in L1000 signature data from package namespace |
+| `diseaseSigs` | Triggered by `CalcDiseaseSig` action button |
+| `debugRelease` | Outputs current `L1000_Release` input value; used as app alive-check in tests |
+
+### UI tab structure
+
+Overview → **Run scFOCAL-dev** (tabsetPanel):
+1. Data Upload — Seurat RDS, assay selection
+2. Exploration — dim plots, cell highlights
+3. Disease Signatures — cell subsetting, heatmap/table/reversal tabs
+4. Drug Response / Synergy Analysis — corrMat upload, compound selection
+
+**Duplicate ID note**: `corrMatUpload` (input) and `referenceCompound_ui` (output) intentionally appear in two tabs — this is existing architecture. Shiny handles duplicate `uiOutput` IDs correctly at runtime. In shinytest2 tests, navigate to the correct tab *before* uploading or reading these elements to avoid "Multiple HTML elements found" warnings.
+
+## Testing Infrastructure
+
+Tests live in `inst/shiny/tests/testthat/`:
+
+- `setup-chromote.R` — raises Chromote's `default_timeout` to 120s; required because the app takes ~12s to load packages on a cold start, which exceeds Chrome's default 10s `Page.navigate` timeout
+- `test-upload.R` — app launch and Seurat upload health checks
+- `test-edge-cases.R` — regression tests for corrMat orientation, gene case normalization, pre-upload navigation crash
+- `fixtures/downsampled_seuratObj.RDS` — 134MB Seurat fixture; requires **Git LFS** before pushing to GitHub
+
+CI: `.github/workflows/shinytest2.yml` runs on every PR to `drug_signature_update`.
+
+## Open Bugs (as of drug_signature_update branch)
+
+- **Bug 1** — `corrMatUpload()` in server.R double-transposes the matrix, swapping drug names and cell barcodes
+- **Bug 2** — Shiny warns about duplicate `corrMatUpload`/`referenceCompound_ui` IDs in tests; workaround by navigating to the correct tab first
+- **Bug 4** — `assay_to_use()` may be called before Seurat upload; needs `req(rdsSeurat())` guard
+- **Bug 5** — Uploaded drug signature CSVs with lowercase gene names produce 0-gene overlap with the Seurat object (which uses uppercase), causing a silent crash; needs `toupper()` normalization

DESCRIPTION

@@ -9,7 +9,7 @@ Description: scFOCAL integrates small molecules transcriptional consensus signat
 License: Custom
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Depends: 
     R (>= 3.5)
 Imports:
@@ -29,6 +29,7 @@ Imports:
     grid,
     htmlwidgets,
     lme4,
+    limma,
     pheatmap,
     plotly,
     reshape2,
@@ -41,3 +42,5 @@ Imports:
     viridis,
     ggpubr,
     ComplexHeatmap
+Suggests: 
+    shinytest2

NAMESPACE

@@ -18,6 +18,7 @@ import(ggrepel)
 import(ggsci)
 import(grid)
 import(htmlwidgets)
+importFrom(limma, lmFit)
 import(lme4)
 import(pheatmap)
 import(plotly)

README.md

@@ -1,3 +1,4 @@
+## Branch to add in new signature files and option for custom drug signature upload (i.e. from TCSgen, in progress) 
 
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