feat: add SCPlotterChat class for chat functionality

Author: pwwang

.Rbuildignore

@@ -1,7 +1,5 @@
 ^LICENSE\.md$
 ^pkgdown\/.+
-^vignettes/articles$
-^vignettes$
 ^CRAN-SUBMISSION$
 ^cran-comments\.md$
 ^docs/\.nojekyll$

.github/workflows/main.yml

@@ -53,11 +53,13 @@ jobs:
           extra-packages: |
             any::devtools, any::pkgdown, any::plotthis, any::ComplexHeatmap,
             any::Seurat, any::concaveman, any::gridGraphics, any::ggVennDiagram,
-            any::clustree, any::ggwordcloud, any::ggalluvial, any::ggpubr,
+            any::clustree, any::ggwordcloud, any::ggalluvial, any::ggpubr, any::callr,
             any::ggforce, any::ggraph, any::ggridges, any::hexbin, any::igraph,
-            any::scattermore, any::ggupset, any::iNEXT, any::metap
+            any::scattermore, any::ggupset, any::iNEXT, any::metap, any::tidyprompt
 
       - uses: r-lib/actions/check-r-package@v2
+        env:
+          OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }}
 
       - name: Install scplotter
         run: |
@@ -67,6 +69,8 @@ jobs:
         run: |
           devtools::document()
           pkgdown::build_site_github_pages(new_process = TRUE, install = TRUE)
+        env:
+          OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }}
 
       - name: Deploy to GitHub pages
         if: github.event_name != 'pull_request'

.gitignore

@@ -2,4 +2,5 @@
 docs/
 *.Rcheck/
 /*.tar.gz
-Rplots.pdf
+Rplots.pdf
+inst/doc

DESCRIPTION

@@ -23,7 +23,8 @@ Imports:
     rlang,
     stringr,
     tidyr,
-    plotthis
+    plotthis,
+    R6
 Suggests:
     ComplexHeatmap,
     Seurat (>= 5.0.0),
@@ -43,7 +44,11 @@ Suggests:
     scattermore,
     gridGraphics,
     iNEXT,
-    metap (>= 1.11)
+    tidyprompt,
+    callr,
+    metap (>= 1.11),
+    knitr,
+    rmarkdown
 LazyData: true
 LazyDataCompression: xz
 Remotes:
@@ -53,3 +58,4 @@ URL: https://github.com/pwwang/scplotter
     https://pwwang.github.io/scplotter/
 BugReports:
     https://github.com/pwwang/scplotter/issues
+VignetteBuilder: knitr

NAMESPACE

@@ -21,12 +21,14 @@ export(FeatureStatPlot)
 export(GSEAPlot)
 export(GSEASummaryPlot)
 export(PrepareEnrichrResult)
+export(SCPlotterChat)
 export(VolcanoPlot)
-export(top)
+import(R6)
 importFrom(SeuratObject,DefaultDimReduc)
 importFrom(SeuratObject,Embeddings)
 importFrom(SeuratObject,GetAssayData)
 importFrom(SeuratObject,Graphs)
+importFrom(SeuratObject,Idents)
 importFrom(SeuratObject,Reductions)
 importFrom(circlize,colorRamp2)
 importFrom(dplyr,"%>%")
@@ -138,5 +140,7 @@ importFrom(tidyr,pivot_wider)
 importFrom(tidyr,replace_na)
 importFrom(tidyr,separate)
 importFrom(tidyr,unite)
+importFrom(tools,parse_Rd)
 importFrom(utils,combn)
 importFrom(utils,getFromNamespace)
+importFrom(utils,help)