Merge pull request #91 from EngyNasr/updatingSuppTables

updating supplementary tables and the table numbers in the script

Author: bebatut

bin/get_data.sh

@@ -10,34 +10,36 @@ wget \
     -O "docs/supplementary/supplementary_table_1.tsv" \
     "https://raw.githubusercontent.com/paulzierep/microgalaxy-survey/refs/heads/main/data/modified_answers.csv" 
 
-
 # Get Codex data
 wget \
     -O "docs/supplementary/supplementary_table_2.tsv" \
     "https://raw.githubusercontent.com/galaxyproject/galaxy_codex/refs/heads/main/communities/microgalaxy/resources/curated_tools.tsv" 
-    
 
+# Get use cases
 wget \
     -O "docs/supplementary/supplementary_table_3.tsv" \
-    "https://raw.githubusercontent.com/galaxyproject/galaxy_codex/refs/heads/main/communities/microgalaxy/resources/curated_workflows.tsv" 
-    
+    "https://docs.google.com/spreadsheets/d/1fGbDFk5u4vwrjcdN8zWXHEvxkLUYJSx_nbK1XUeSZyk/export?format=tsv"  
 
+# Get tool suites number of figure 3
 wget \
     -O "docs/supplementary/supplementary_table_4.tsv" \
-    "https://raw.githubusercontent.com/galaxyproject/galaxy_codex/refs/heads/main/communities/microgalaxy/resources/tutorials.tsv" 
-    
+    "https://docs.google.com/spreadsheets/d/1iG7qXbiMUrQsPxVuIXAvDgyrGK9PWyWpxy1IyDCB2TQ/export?format=tsv"  
 
-# Get training events
+# Get workflows table
 wget \
     -O "docs/supplementary/supplementary_table_5.tsv" \
-    "https://docs.google.com/spreadsheets/d/1Eejqmb4CJQnyy51ayLMOgTPf5mHArKlCtSYzEsFNc2s/export?format=tsv&gid=0" 
+    "https://raw.githubusercontent.com/galaxyproject/galaxy_codex/refs/heads/main/communities/microgalaxy/resources/curated_workflows.tsv" 
 
-
-# Get use cases
+# Get tutorials table
 wget \
     -O "docs/supplementary/supplementary_table_6.tsv" \
-    "https://docs.google.com/spreadsheets/d/1fGbDFk5u4vwrjcdN8zWXHEvxkLUYJSx_nbK1XUeSZyk/export?format=tsv&gid=1847337048" 
-
+    "https://raw.githubusercontent.com/galaxyproject/galaxy_codex/refs/heads/main/communities/microgalaxy/resources/tutorials.tsv" 
+    
+# Get training events
+wget \
+    -O "docs/supplementary/supplementary_table_7.tsv" \
+    "https://docs.google.com/spreadsheets/d/1Eejqmb4CJQnyy51ayLMOgTPf5mHArKlCtSYzEsFNc2s/export?format=tsv&gid=0" 
+     
 # Get Supplementary documents
 wget \
     -O "docs/supplementary/supplementary_document_1.pdf" \

bin/statistics_calculations.ipynb

@@ -44,13 +44,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "tutorials_url = \"../docs/supplementary/supplementary_table_4.tsv\"\n",
+    "tutorials_url = \"../docs/supplementary/supplementary_table_6.tsv\"\n",
     "tools_url = \"../docs/supplementary/supplementary_table_2.tsv\"\n",
-    "workflows_url = \"../docs/supplementary/supplementary_table_3.tsv\"\n",
+    "workflows_url = \"../docs/supplementary/supplementary_table_5.tsv\"\n",
     "\n",
     "tutorials_df = pd.read_csv(tutorials_url, sep=\"\\t\")\n",
     "tutorials_df = tutorials_df.drop_duplicates(keep=\"last\")\n",

bin/tools-graphs.Rmd

@@ -37,8 +37,8 @@ library(colorspace)
 ## RUN ON CONSOLE IN THIS CASE
 
 tools_url     <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_2.tsv"
-workflows_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_3.tsv"
-tutorials_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_4.tsv"
+workflows_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_5.tsv"
+tutorials_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_6.tsv"
 
 tools_dt     <- tools_url |> fread()
 workflows_dt <- workflows_url |> fread()
@@ -961,7 +961,7 @@ save_plot <- function(plot, filename, w, h) {
     
 }
 
-save_plot(multi, "../docs/extended/figure_3", 10, 12)
+save_plot(multi, "../docs/extended/figure_2", 10, 12)
 
 # ggsave(
 #     plot = multi, filename = paste0(outfolder, "/extended_figure_3.png"),

bin/tutorials-graphs.Rmd

@@ -38,7 +38,7 @@ library(packcircles)
 ## THERE IS A BUG UNFORTUNATELY WITH fread FUNCTION
 ## RUN ON CONSOLE IN THIS CASE
 
-microGalaxy_tutorials_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_4.tsv"
+microGalaxy_tutorials_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_6.tsv"
 microGalaxy_tools_url     <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_2.tsv"
 # all_tools_url             <- "https://raw.githubusercontent.com/galaxyproject/galaxy_codex/refs/heads/main/communities/all/resources/tools.tsv"
 

bin/workflows-graphs.Rmd

@@ -38,7 +38,7 @@ library(packcircles)
 ## THERE IS A BUG UNFORTUNATELY WITH fread FUNCTION
 ## RUN ON CONSOLE IN THIS CASE
 
-workflows_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_3.tsv"
+workflows_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_5.tsv"
 all_tools_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_2.tsv"
 
 workflows_dt <- workflows_url |> fread(sep = "\t")