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✨ Add config files in the documentation and modify the headers of notebooks and config files
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‎docs/example_report.md‎

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# Vuegen Case Study - View HTML Report
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# Earth Microbiome Project Case Study - HTML and Streamlit Example Reports
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The stable version of the current `html` report generated in the example notebook
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using `vuegen` can be viewed at
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[multiomics-analytics-group.github.io/vuegen/](https://multiomics-analytics-group.github.io/vuegen/)
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The Earth Microbiome Project case study generated in the example notebook using `vuegen` is available online as [HTML](https://multiomics-analytics-group.github.io/vuegen/) and [Streamlit](https://earth-microbiome-vuegen-demo.streamlit.app/) reports.

‎docs/index.md‎

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:caption: Building a report
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vuegen_basic_case_study
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vuegen_basic_case_study_configfile
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vuegen_case_study_earth_microbiome
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vuegen_case_study_earth_microbiome_configfile
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vuegen_APICall_configfile
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vuegen_Chatbot_configfile
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example_report
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```
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‎docs/vuegen_APICall_configfile.md‎

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# APICall Component Configuration File
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A [configuration file](https://github.com/Multiomics-Analytics-Group/vuegen/blob/main/docs/example_config_files/APIcall_example_config.yaml) for the API call component is provided below:
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```yaml
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report:
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title: APICall example
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description: An APICall example.
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sections:
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- title: APICall test
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subsections:
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- title: JSONPlaceholder test
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components:
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- title: GET request
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component_type: apicall
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api_url: https://jsonplaceholder.typicode.com/todos/1
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method: GET
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- title: POST request
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component_type: apicall
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api_url: https://jsonplaceholder.typicode.com/todos
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method: POST
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request_body: |
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{
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"userId": 1,
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"title": "Go running",
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"completed": false
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}
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- title: PUT request
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component_type: apicall
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api_url: https://jsonplaceholder.typicode.com/todos/10
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method: PUT
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request_body: |
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{
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"userId": 1,
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"title": "Play the guitar",
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"completed": true
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}
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- title: PATCH request
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component_type: apicall
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api_url: https://jsonplaceholder.typicode.com/todos/10
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method: PATCH
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request_body: |
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{
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"title": "Go for a hike"
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}
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- title: DELETE request
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component_type: apicall
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api_url: https://jsonplaceholder.typicode.com/todos/10
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method: DELETE
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```

‎docs/vuegen_Chatbot_configfile.md‎

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# Chatbot Component Configuration File
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A [configuration file](https://github.com/Multiomics-Analytics-Group/vuegen/blob/main/docs/example_config_files/Chatbot_example_config.yaml) for the Chatbot component is provided below:
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```yaml
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report:
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title: Chatbot example
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description: >
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A chatbot exaple.
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sections:
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- title: ChatBot test
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subsections:
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- title: Simple test
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components:
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- title: ChatBot test
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component_type: chatbot
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api_url: http://localhost:11434/api/chat
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model: llama3.2
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```

‎docs/vuegen_basic_case_study.ipynb‎

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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Vuegen Basic Case Study - Predefined Directory\n",
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"# Predefined Directory Case Study - Notebook\n",
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"\n",
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"[![Open In Colab][colab_badge]][colab_link]\n",
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"\n",

‎docs/vuegen_basic_case_study_configfile.md‎

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# Predefined Directory Case Study - Configuration File
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The [configuration file](https://github.com/Multiomics-Analytics-Group/vuegen/blob/main/docs/example_config_files/Basic_example_vuegen_demo_notebook_config.yaml) of the basic case study using a predefined directory is presented below:
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```yaml
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report:
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title: Basic Example Vuegen Demo Notebook
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description: A general description of the report.
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graphical_abstract: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg
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logo: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg
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sections:
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- title: Plots
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description: This section contains example plots.
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subsections:
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- title: Interactive Plots
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description: Optional description for section.
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components:
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- title: Top Species Plot By Biome Plotly
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file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/1_top_species_plot_by_biome_plotly.json
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description: ''
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caption: ''
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component_type: plot
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plot_type: plotly
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- title: Multiline Plot Altair
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file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/2_multiline_plot_altair.json
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description: ''
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caption: ''
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component_type: plot
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plot_type: altair
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- title: Pie Plot Countries Plotly
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file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/3_pie_plot_countries_plotly.json
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description: ''
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caption: ''
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component_type: plot
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plot_type: plotly
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- title: Pie Plots Biomes Plotly
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file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/4_pie_plots_biomes_plotly.json
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description: ''
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caption: ''
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component_type: plot
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plot_type: plotly
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- title: Saline Metagenomics Samples Map Altair
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file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/5_saline_metagenomics_samples_map_altair.json
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description: ''
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caption: ''
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component_type: plot
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plot_type: altair
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- title: Description
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file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/description.md
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description: ''
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caption: ''
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component_type: markdown
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- title: Static Plots
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description: ''
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components:
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- title: Number Samples Per Study
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file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/2_Static_plots/1_number_samples_per_study.png
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description: ''
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caption: ''
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component_type: plot
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plot_type: static
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- title: Animal Metagenomics Samples Map
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file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/2_Static_plots/2_animal_metagenomics_samples_map.png
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description: ''
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caption: ''
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component_type: plot
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plot_type: static
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- title: Alpha Diversity Host Associated Samples
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file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/2_Static_plots/3_alpha_diversity_host_associated_samples.png
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description: ''
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caption: ''
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component_type: plot
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plot_type: static
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- title: "Graphical overview of VueGen workflow and components"
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file_path: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_graph_abstract.png
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description: ''
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caption: The diagram illustrates the processing pipeline of VueGen, starting
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from either a directory or a YAML configuration file. Reports consist of hierarchical
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sections and subsections, each containing various components such as plots,
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dataframes, Markdown, HTML, and data retrieved via API calls.
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component_type: plot
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plot_type: static
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- title: Dataframes
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description: ''
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subsections:
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- title: All Formats
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description: This subsection contains example dataframes.
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components:
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- title: Phyla Correlation Network Csv
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file_path: example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/1_phyla_correlation_network_csv.csv
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description: ''
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caption: ''
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component_type: dataframe
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file_format: csv
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delimiter: ','
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- title: Abundance Table Example Xls
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file_path: example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/2_abundance_table_example_xls.xls
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description: ''
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caption: ''
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component_type: dataframe
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file_format: xls
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- title: Sample Info Example Txt
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file_path: example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/3_sample_info_example_txt.txt
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description: ''
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caption: ''
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component_type: dataframe
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file_format: txt
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delimiter: \t
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- title: Sample Info Example Parquet
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file_path: example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/4_sample_info_example_parquet.parquet
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description: ''
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caption: ''
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component_type: dataframe
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file_format: parquet
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- title: Networks
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description: ''
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subsections:
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- title: Interactive Networks
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description: Optional description for subsection
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components:
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- title: Man Example
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file_path: example_data/Basic_example_vuegen_demo_notebook/3_Networks/1_Interactive_networks/1_man_example.graphml
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description: ''
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caption: ''
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component_type: plot
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plot_type: interactive_network
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- title: Description
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file_path: example_data/Basic_example_vuegen_demo_notebook/3_Networks/1_Interactive_networks/description.md
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description: ''
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caption: ''
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component_type: markdown
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- title: Static Networks
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description: ''
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components:
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- title: Phyla Correlation Network
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file_path: example_data/Basic_example_vuegen_demo_notebook/3_Networks/2_Static_networks/1_phyla_correlation_network.png
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description: ''
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caption: ''
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component_type: plot
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plot_type: static
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- title: Html
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description: ''
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subsections:
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- title: All Html
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description: ''
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components:
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- title: Plot
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file_path: example_data/Basic_example_vuegen_demo_notebook/4_Html/1_All_html/1_plot.html
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description: ''
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caption: ''
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component_type: html
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- title: Ckg Network
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file_path: example_data/Basic_example_vuegen_demo_notebook/4_Html/1_All_html/2_ckg_network.html
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description: ''
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caption: ''
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component_type: plot
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plot_type: interactive_network
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- title: Multiqc Report
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file_path: example_data/Basic_example_vuegen_demo_notebook/4_Html/1_All_html/3_multiqc_report.html
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description: ''
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caption: ''
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component_type: html
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- title: Markdown
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description: ''
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subsections:
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- title: All Markdown
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description: ''
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components:
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- title: Readme
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file_path: example_data/Basic_example_vuegen_demo_notebook/5_Markdown/1_All_markdown/README.md
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description: ''
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caption: ''
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component_type: markdown
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```
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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).

‎docs/vuegen_case_study_earth_microbiome.ipynb‎

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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Vuegen Case Study - Earth Microbiome Project\n",
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"# Earth Microbiome Project Case Study - Notebook\n",
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"\n",
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"[![Open In Colab][colab_badge]][colab_link]\n",
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"\n",

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