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📝 Docs: Add example config files and remove unnecessary images
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‎docs/example_config_files/APIcall_example_config.yaml‎

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report:
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title: APICall example
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description: An APICall exaple.
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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: JSONPlaceholder component
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component_type: apicall
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api_url: https://jsonplaceholder.typicode.com/todos/1

‎docs/example_config_files/Basic_example_vuegen_demo_notebook_config.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

‎docs/example_config_files/Chatbot_example_config.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

‎docs/example_config_files/Earth_microbiome_vuegen_demo_notebook_config.yaml‎

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report:
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title: Earth Microbiome Vuegen Demo Notebook
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description: "The Earth Microbiome Project (EMP) is a systematic attempt to characterize\
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\ global microbial taxonomic and functional diversity for the benefit of the planet\
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\ and humankind. \n It aimed to sample the Earth\u2019s microbial communities\
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\ at an unprecedented scale in order to advance our understanding of the organizing\
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\ biogeographic principles that govern microbial community structure. \n The\
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\ EMP dataset is generated from samples that individual researchers have compiled\
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\ and contributed to the EMP. \n The result is both a reference database giving\
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\ global context to DNA sequence data and a framework for incorporating data from\
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\ future studies, fostering increasingly complete characterization of Earth\u2019\
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s microbial diversity.\n \n You can find more information about the Earth Microbiome\
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\ Project at https://earthmicrobiome.org/ and in the [original article](https://www.nature.com/articles/nature24621).\n"
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graphical_abstract: https://raw.githubusercontent.com/ElDeveloper/cogs220/master/emp-logo.svg
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logo: https://raw.githubusercontent.com/ElDeveloper/cogs220/master/emp-logo.svg
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sections:
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- title: Exploratory Data Analysis
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description: This section contains the exploratory data analysis of the Earth Microbiome
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Project (EMP) dataset.
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subsections:
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- title: Sample Exploration
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description: ''
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components:
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- title: Metadata Random Subset
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file_path: example_data/Earth_microbiome_vuegen_demo_notebook/1_Exploratory_data_analysis/1_sample_exploration/1_metadata_random_subset.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: Animal Samples Map
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file_path: example_data/Earth_microbiome_vuegen_demo_notebook/1_Exploratory_data_analysis/1_sample_exploration/2_animal_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: Plant Samples Map
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file_path: example_data/Earth_microbiome_vuegen_demo_notebook/1_Exploratory_data_analysis/1_sample_exploration/3_plant_samples_map.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 Samples Map
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file_path: example_data/Earth_microbiome_vuegen_demo_notebook/1_Exploratory_data_analysis/1_sample_exploration/4_saline_samples_map.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: Physicochemical properties of the EMP samples
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file_path: https://raw.githubusercontent.com/biocore/emp/master/methods/images/figureED1_physicochemical.png
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description: ''
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caption: Pairwise scatter plots of available physicochemical metadat are shown
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for temperature, salinity, oxygen, and pH, and for phosphate, nitrate, and
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ammonium
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component_type: PLOT
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plot_type: STATIC
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- title: Metagenomics
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description: ''
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subsections:
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- title: Alpha Diversity
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description: This subsection contains the alpha diversity analysis of the EMP
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dataset.
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components:
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- title: Alpha Diversity Host Associated Samples
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file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/1_alpha_diversity/1_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: Alpha Diversity Free Living Samples
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file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/1_alpha_diversity/2_alpha_diversity_free_living_samples.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: Average Copy Number
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description: ''
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components:
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- title: Average Copy Number Emp Ontology Level2
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file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/2_average_copy_number/1_average_copy_number_emp_ontology_level2.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: Average Copy Number Emp Ontology Level3
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file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/2_average_copy_number/2_average_copy_number_emp_ontology_level3.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: Nestedness
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description: ''
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components:
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- title: Nestedness Random Subset
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file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/1_nestedness_random_subset.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: All Samples
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file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/2_all_samples.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: Plant Samples
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file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/3_plant_samples.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: Animal Samples
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file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/4_animal_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: Non Saline Samples
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file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/5_non_saline_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: Shanon entropy analysis
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description: This subsection contains the Shannon entropy analysis of the EMP
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dataset.
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components:
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- title: Specificity of sequences and higher taxonomic groups for environment
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file_path: https://raw.githubusercontent.com/biocore/emp/master/methods/images/figure4_entropy.png
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description: ''
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caption: a) Environment distribution in all genera and 400 randomly chosen tag
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sequence. b) and c) Shannon entropy within each taxonomic group.
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component_type: PLOT
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plot_type: STATIC
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- title: Network Analysis
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description: ''
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subsections:
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- title: Phyla Association Networks
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description: ''
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components:
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- title: Phyla Counts Subset
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file_path: example_data/Earth_microbiome_vuegen_demo_notebook/3_Network_analysis/1_phyla_association_networks/1_phyla_counts_subset.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: Phyla Correlation Network With 0.5 Threshold Edgelist
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file_path: example_data/Earth_microbiome_vuegen_demo_notebook/3_Network_analysis/1_phyla_association_networks/2_phyla_correlation_network_with_0.5_threshold_edgelist.csv
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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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csv_network_format: EDGELIST
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- title: Phyla Correlation Network With 0.5 Threshold
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file_path: example_data/Earth_microbiome_vuegen_demo_notebook/3_Network_analysis/1_phyla_association_networks/3_phyla_correlation_network_with_0.5_threshold.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

‎docs/example_data/Earth_microbiome_vuegen_demo_notebook/emp_deblur_100bp.subset_2k.rare_5000.biom‎

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‎docs/example_data/Earth_microbiome_vuegen_demo_notebook/emp_logo.png‎

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‎docs/example_data/mona_logo.png‎

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