📝 Update md files for the yaml examples on the documentation

sayalaruano · sayalaruano · commit f66f8b8aee11 · 2025-06-30T12:17:44.000+02:00
diff --git a/docs/vuegen_basic_case_study_configfile.md b/docs/vuegen_basic_case_study_configfile.md
@@ -6,172 +6,171 @@ The [configuration file](https://github.com/Multiomics-Analytics-Group/vuegen/bl
 report:
   title: Basic Example Vuegen Demo Notebook
   description: A general description of the report.
-  graphical_abstract: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg
-  logo: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg
+  graphical_abstract: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.png
+  logo: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.png
 sections:
-  - title: Plots
-    description: This section contains example plots.
-    subsections:
-      - title: Interactive Plots
-        description: Optional description for section.
-        components:
-          - title: Top Species Plot By Biome Plotly
-            file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/1_top_species_plot_by_biome_plotly.json
-            description: ""
-            caption: ""
-            component_type: plot
-            plot_type: plotly
-          - title: Multiline Plot Altair
-            file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/2_multiline_plot_altair.json
-            description: ""
-            caption: ""
-            component_type: plot
-            plot_type: altair
-          - title: Pie Plot Countries Plotly
-            file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/3_pie_plot_countries_plotly.json
-            description: ""
-            caption: ""
-            component_type: plot
-            plot_type: plotly
-          - title: Pie Plots Biomes Plotly
-            file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/4_pie_plots_biomes_plotly.json
-            description: ""
-            caption: ""
-            component_type: plot
-            plot_type: plotly
-          - title: Saline Metagenomics Samples Map Altair
-            file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/5_saline_metagenomics_samples_map_altair.json
-            description: ""
-            caption: ""
-            component_type: plot
-            plot_type: altair
-          - title: Description
-            file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/description.md
-            description: ""
-            caption: ""
-            component_type: markdown
-      - title: Static Plots
-        description: ""
-        components:
-          - title: Number Samples Per Study
-            file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/2_Static_plots/1_number_samples_per_study.png
-            description: ""
-            caption: ""
-            component_type: plot
-            plot_type: static
-          - title: Animal Metagenomics Samples Map
-            file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/2_Static_plots/2_animal_metagenomics_samples_map.png
-            description: ""
-            caption: ""
-            component_type: plot
-            plot_type: static
-          - title: Alpha Diversity Host Associated Samples
-            file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/2_Static_plots/3_alpha_diversity_host_associated_samples.png
-            description: ""
-            caption: ""
-            component_type: plot
-            plot_type: static
-          - title: "Graphical overview of VueGen workflow and components"
-            file_path: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_graph_abstract.png
-            description: ""
-            caption:
-              The diagram illustrates the processing pipeline of VueGen, starting
-              from either a directory or a YAML configuration file. Reports consist of hierarchical
-              sections and subsections, each containing various components such as plots,
-              dataframes, Markdown, HTML, and data retrieved via API calls.
-            component_type: plot
-            plot_type: static
-  - title: Dataframes
-    description: ""
-    subsections:
-      - title: All Formats
-        description: This subsection contains example dataframes.
-        components:
-          - title: Phyla Correlation Network Csv
-            file_path: example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/1_phyla_correlation_network_csv.csv
-            description: ""
-            caption: ""
-            component_type: dataframe
-            file_format: csv
-            delimiter: ","
-          - title: Abundance Table Example Xls
-            file_path: example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/2_abundance_table_example_xls.xls
-            description: ""
-            caption: ""
-            component_type: dataframe
-            file_format: xls
-          - title: Sample Info Example Txt
-            file_path: example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/3_sample_info_example_txt.txt
-            description: ""
-            caption: ""
-            component_type: dataframe
-            file_format: txt
-            delimiter: \t
-          - title: Sample Info Example Parquet
-            file_path: example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/4_sample_info_example_parquet.parquet
-            description: ""
-            caption: ""
-            component_type: dataframe
-            file_format: parquet
-  - title: Networks
-    description: ""
-    subsections:
-      - title: Interactive Networks
-        description: Optional description for subsection
-        components:
-          - title: Man Example
-            file_path: example_data/Basic_example_vuegen_demo_notebook/3_Networks/1_Interactive_networks/1_man_example.graphml
-            description: ""
-            caption: ""
-            component_type: plot
-            plot_type: interactive_network
-          - title: Description
-            file_path: example_data/Basic_example_vuegen_demo_notebook/3_Networks/1_Interactive_networks/description.md
-            description: ""
-            caption: ""
-            component_type: markdown
-      - title: Static Networks
-        description: ""
-        components:
-          - title: Phyla Correlation Network
-            file_path: example_data/Basic_example_vuegen_demo_notebook/3_Networks/2_Static_networks/1_phyla_correlation_network.png
-            description: ""
-            caption: ""
-            component_type: plot
-            plot_type: static
-  - title: Html
-    description: ""
-    subsections:
-      - title: All Html
-        description: ""
-        components:
-          - title: Plot
-            file_path: example_data/Basic_example_vuegen_demo_notebook/4_Html/1_All_html/1_plot.html
-            description: ""
-            caption: ""
-            component_type: html
-          - title: Ckg Network
-            file_path: example_data/Basic_example_vuegen_demo_notebook/4_Html/1_All_html/2_ckg_network.html
-            description: ""
-            caption: ""
-            component_type: plot
-            plot_type: interactive_network
-          - title: Multiqc Report
-            file_path: example_data/Basic_example_vuegen_demo_notebook/4_Html/1_All_html/3_multiqc_report.html
-            description: ""
-            caption: ""
-            component_type: html
-  - title: Markdown
-    description: ""
-    subsections:
-      - title: All Markdown
-        description: ""
-        components:
-          - title: Readme
-            file_path: example_data/Basic_example_vuegen_demo_notebook/5_Markdown/1_All_markdown/README.md
-            description: ""
-            caption: ""
-            component_type: markdown
+- title: Plots
+  description: This section contains example plots.
+  subsections:
+  - title: Interactive Plots
+    description: Optional description for section.
+    components:
+    - title: Top Species Plot By Biome Plotly
+      file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/1_top_species_plot_by_biome_plotly.json
+      description: ''
+      caption: ''
+      component_type: plot
+      plot_type: plotly
+    - title: Multiline Plot Altair
+      file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/2_multiline_plot_altair.json
+      description: ''
+      caption: ''
+      component_type: plot
+      plot_type: altair
+    - title: Pie Plot Countries Plotly
+      file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/3_pie_plot_countries_plotly.json
+      description: ''
+      caption: ''
+      component_type: plot
+      plot_type: plotly
+    - title: Pie Plots Biomes Plotly
+      file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/4_pie_plots_biomes_plotly.json
+      description: ''
+      caption: ''
+      component_type: plot
+      plot_type: plotly
+    - title: Saline Metagenomics Samples Map Altair
+      file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/5_saline_metagenomics_samples_map_altair.json
+      description: ''
+      caption: ''
+      component_type: plot
+      plot_type: altair
+    - title: Description
+      file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/description.md
+      description: ''
+      caption: ''
+      component_type: markdown
+  - title: Static Plots
+    description: ''
+    components:
+    - title: Number Samples Per Study
+      file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/2_Static_plots/1_number_samples_per_study.png
+      description: ''
+      caption: ''
+      component_type: plot
+      plot_type: static
+    - title: Animal Metagenomics Samples Map
+      file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/2_Static_plots/2_animal_metagenomics_samples_map.png
+      description: ''
+      caption: ''
+      component_type: plot
+      plot_type: static
+    - title: Alpha Diversity Host Associated Samples
+      file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/2_Static_plots/3_alpha_diversity_host_associated_samples.png
+      description: ''
+      caption: ''
+      component_type: plot
+      plot_type: static
+    - title: "Graphical overview of VueGen workflow and components"
+      file_path: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_graph_abstract.png
+      description: ''
+      caption: The diagram illustrates the processing pipeline of VueGen, starting
+        from either a directory or a YAML configuration file. Reports consist of hierarchical
+        sections and subsections, each containing various components such as plots,
+        dataframes, Markdown, HTML, and data retrieved via API calls.
+      component_type: plot
+      plot_type: static
+- title: Dataframes
+  description: ''
+  subsections:
+  - title: All Formats
+    description: This subsection contains example dataframes.
+    components:
+    - title: Phyla Correlation Network Csv
+      file_path: example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/1_phyla_correlation_network_csv.csv
+      description: ''
+      caption: ''
+      component_type: dataframe
+      file_format: csv
+      delimiter: ','
+    - title: Abundance Table Example Xls
+      file_path: example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/2_abundance_table_example_xls.xls
+      description: ''
+      caption: ''
+      component_type: dataframe
+      file_format: xls
+    - title: Sample Info Example Txt
+      file_path: example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/3_sample_info_example_txt.txt
+      description: ''
+      caption: ''
+      component_type: dataframe
+      file_format: txt
+      delimiter: \t
+    - title: Sample Info Example Parquet
+      file_path: example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/4_sample_info_example_parquet.parquet
+      description: ''
+      caption: ''
+      component_type: dataframe
+      file_format: parquet
+- title: Networks
+  description: ''
+  subsections:
+  - title: Interactive Networks
+    description: Optional description for subsection
+    components:
+    - title: Man Example
+      file_path: example_data/Basic_example_vuegen_demo_notebook/3_Networks/1_Interactive_networks/1_man_example.graphml
+      description: ''
+      caption: ''
+      component_type: plot
+      plot_type: interactive_network
+    - title: Description
+      file_path: example_data/Basic_example_vuegen_demo_notebook/3_Networks/1_Interactive_networks/description.md
+      description: ''
+      caption: ''
+      component_type: markdown
+  - title: Static Networks
+    description: ''
+    components:
+    - title: Phyla Correlation Network
+      file_path: example_data/Basic_example_vuegen_demo_notebook/3_Networks/2_Static_networks/1_phyla_correlation_network.png
+      description: ''
+      caption: ''
+      component_type: plot
+      plot_type: static
+- title: Html
+  description: ''
+  subsections:
+  - title: All Html
+    description: ''
+    components:
+    - title: Plot
+      file_path: example_data/Basic_example_vuegen_demo_notebook/4_Html/1_All_html/1_plot.html
+      description: ''
+      caption: ''
+      component_type: html
+    - title: Ckg Network
+      file_path: example_data/Basic_example_vuegen_demo_notebook/4_Html/1_All_html/2_ckg_network.html
+      description: ''
+      caption: ''
+      component_type: plot
+      plot_type: interactive_network
+    - title: Multiqc Report
+      file_path: example_data/Basic_example_vuegen_demo_notebook/4_Html/1_All_html/3_multiqc_report.html
+      description: ''
+      caption: ''
+      component_type: html
+- title: Markdown
+  description: ''
+  subsections:
+  - title: All Markdown
+    description: ''
+    components:
+    - title: Readme
+      file_path: example_data/Basic_example_vuegen_demo_notebook/5_Markdown/1_All_markdown/README.md
+      description: ''
+      caption: ''
+      component_type: markdown
 ```
 
 The directory with he example data is available in the [GitHub repository](https://github.com/Multiomics-Analytics-Group/vuegen/blob/main/docs/example_data/Basic_example_vuegen_demo_notebook).
diff --git a/docs/vuegen_earth_microbiome_case_study_configfile.md b/docs/vuegen_earth_microbiome_case_study_configfile.md
@@ -128,8 +128,7 @@ sections:
       component_type: PLOT
       plot_type: STATIC
   - title: Shanon entropy analysis
-    description: This subsection contains the Shannon entropy analysis of the EMP
-    dataset.
+    description: This subsection contains the Shannon entropy analysis of the EMP dataset.
     components:
     - title: Specificity of sequences and higher taxonomic groups for environment
       file_path: https://raw.githubusercontent.com/biocore/emp/master/methods/images/figure4_entropy.png
