Deploying to gh-pages from @ 98de442 🚀

Author: pwwang

articles/Visualizing_data_with_LLMs.html

@@ -215,7 +215,7 @@ chat$ask("Generate a cell-cell communication plot for the cellphonedb_res data."
 #> required to skim dataframes. Skim summary of dataframes currently not shown in
 #> prompt
 #> Code ran:
-#> CCCPlot(data = cellphonedb_res, plot_type = "dot")
+#> CCCPlot(cellphonedb_res)
 ```
 
 ![](Visualizing_data_with_LLMs_files/figure-html/unnamed-chunk-6-1.png)
@@ -246,7 +246,7 @@ chat$ask("Add a proper title to the plot")
 #> required to skim dataframes. Skim summary of dataframes currently not shown in
 #> prompt
 #> Code ran:
-#> CCCPlot(cellphonedb_res, plot_type = "heatmap", title = "Cell-Cell Communication Heatmap (LIANA)")
+#> CCCPlot(cellphonedb_res, title = "Cell-Cell Communication Plot (cellphonedb_res)")
 ```
 
 ![](Visualizing_data_with_LLMs_files/figure-html/unnamed-chunk-8-1.png)
@@ -255,12 +255,12 @@ chat$ask("Add a proper title to the plot")
 # To fetch the previous conversation
 # Note that the response from the LLM is simplified in the history
 chat$get_history()
-#> [1] "User: Generate a cell-cell communication plot for the cellphonedb_res data."                                                                                                
-#> [2] "Assistant: tool - CCCPlot; data - scplotter::cellphonedb_res; code - CCCPlot(data = cellphonedb_res, plot_type = \"dot\")"                                                  
-#> [3] "User: Do a heatmap instead"                                                                                                                                                 
-#> [4] "Assistant: tool - CCCPlot; data - scplotter::cellphonedb_res; code - CCCPlot(cellphonedb_res, plot_type = \"heatmap\")"                                                     
-#> [5] "User: Add a proper title to the plot"                                                                                                                                       
-#> [6] "Assistant: tool - CCCPlot; data - scplotter::cellphonedb_res; code - CCCPlot(cellphonedb_res, plot_type = \"heatmap\", title = \"Cell-Cell Communication Heatmap (LIANA)\")"
+#> [1] "User: Generate a cell-cell communication plot for the cellphonedb_res data."                                                                              
+#> [2] "Assistant: tool - CCCPlot; data - scplotter::cellphonedb_res; code - CCCPlot(cellphonedb_res)"                                                            
+#> [3] "User: Do a heatmap instead"                                                                                                                               
+#> [4] "Assistant: tool - CCCPlot; data - scplotter::cellphonedb_res; code - CCCPlot(cellphonedb_res, plot_type = \"heatmap\")"                                   
+#> [5] "User: Add a proper title to the plot"                                                                                                                     
+#> [6] "Assistant: tool - CCCPlot; data - scplotter::cellphonedb_res; code - CCCPlot(cellphonedb_res, title = \"Cell-Cell Communication Plot (cellphonedb_res)\")"
 
 # To clear the history
 chat$clear_history()
@@ -1250,11 +1250,11 @@ chat$ask("Generate a cell-cell communication plot for the cellphonedb_res data."
     #> --- Receiving response from LLM provider: ---
 
     #> ```r
-    #> CCCPlot(data = cellphonedb_res, plot_type = "dot")
+    #> CCCPlot(cellphonedb_res, plot_type = "network", legend.position = "none")
     #> ```
 
     #> Code ran:
-    #> CCCPlot(data = cellphonedb_res, plot_type = "dot")
+    #> CCCPlot(cellphonedb_res, plot_type = "network", legend.position = "none")
 
 ![](Visualizing_data_with_LLMs_files/figure-html/unnamed-chunk-10-1.png)
 
@@ -2239,10 +2239,10 @@ chat$ask("Generate a cell-cell communication plot for the cellphonedb_res data."
     #> --- Receiving response from LLM provider: ---
 
     #> ```r
-    #> CCCPlot(cellphonedb_res, plot_type = "network")
+    #> CCCPlot(cellphonedb_res, plot_type = "network", legend.position = "none")
     #> ```
 
     #> Code ran:
-    #> CCCPlot(cellphonedb_res, plot_type = "network")
+    #> CCCPlot(cellphonedb_res, plot_type = "network", legend.position = "none")
 
 ![](Visualizing_data_with_LLMs_files/figure-html/unnamed-chunk-11-1.png)

articles/Visualizing_data_with_LLMs.md

@@ -20,7 +20,7 @@ articles:
   articles/Seurat_Xenium: Seurat_Xenium.html
   Visualizing_data_with_LLMs: Visualizing_data_with_LLMs.html
   Working_with_anndata_h5ad_files: Working_with_anndata_h5ad_files.html
-last_built: 2026-01-14T18:05Z
+last_built: 2026-01-15T04:05Z
 urls:
   reference: https://pwwang.github.io/scplotter/reference
   article: https://pwwang.github.io/scplotter/articles

articles/Visualizing_data_with_LLMs_files/figure-html/unnamed-chunk-10-1.png

@@ -123,9 +123,9 @@ ne(
   return_ids = NULL
 )
 
-and(x, y)
+and(x, y, ...)
 
-or(x, y)
+or(x, y, ...)
 ```
 
 ## Arguments
@@ -205,7 +205,7 @@ or(x, y)
 
 - ...:
 
-  More groups to compare.
+  Additional vectors to compare in logical operations (and/or).
 
 - include_zeros: