Earth Microbiome Project Case Study - Configuration File

The configuration file of the Earth Microbiome Project case study is shown below:

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

The directory with he example data is available in the GitHub repository.