The configuration file of the basic case study using a predefined directory is presented below:
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.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: markdownThe directory with he example data is available in the GitHub repository.