Improve the docs (#96)

* wip improving the docs * update sidebar * update team
openpipelines-bio · Aug 30, 2024 · 574a534 · 574a534
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diff --git a/_quarto.yml b/_quarto.yml
@@ -33,33 +33,29 @@ website:
         url: https://github.com/openpipelines-bio/openpipeline
         aria-label: GitHub
   sidebar:
-    - id: components
-      title: Components
+    - id: reference
+      title: Reference
+      contents: components
+      collapse-level: 3
+    - id: guide
+      title: Guide
       contents:
-        - components
-        - text: Workflows
+        - id: fundamentals
           collapse-level: 3
-          contents: components/workflows/**
-        - text: Modules
+          section: Fundamentals
+          contents: fundamentals/*
+        - id: user_guide
+          section: User guide
           collapse-level: 3
-          contents:
-            - auto: components/modules/**
-    - id: user_guide
-      collapse-level: 3
-      title: User guide
-      contents: user_guide
-    - id: fundamentals
-      collapse-level: 3
-      title: Fundamentals
-      contents: fundamentals
-    - id: contributing
-      collapse-level: 3
-      title: Contributing
-      contents: contributing
-    - id: more_information
-      collapse-level: 3
-      title: More information
-      contents: more_information
+          contents: user_guide/*
+        - id: contributing
+          collapse-level: 3
+          section: Contributing
+          contents: contributing/*
+        - id: more_information
+          collapse-level: 3
+          section: More information
+          contents: more_information/*
 
 format:
   html:

diff --git a/components/index.qmd b/components/index.qmd
@@ -4,15 +4,15 @@ description: An overview of the workflows and modules in OpenPipelines
 listing:
   - id: workflows
     type: table
-    contents: "workflows/**/*.qmd"
+    contents: "workflows/*/*.qmd"
     fields: [title, namespace, description]
     field-display-names: 
         title: Name
         namespace: Namespace
         description: Description
   - id: modules
     type: table
-    contents: "modules/**/*.qmd"
+    contents: "modules/*/*.qmd"
     fields: [title, namespace, description]
     field-display-names: 
         title: Name

diff --git a/components/modules/index.qmd b/components/modules/index.qmd
@@ -0,0 +1,20 @@
+---
+title: "Modules"
+description: An overview of the modules in OpenPipelines
+order: 60
+listing:
+  - id: modules
+    type: table
+    contents: "**.qmd"
+    fields: [title, namespace, description]
+    field-display-names: 
+        title: Name
+        namespace: Namespace
+        description: Description
+---
+
+
+## Modules
+
+:::{#modules}
+:::
diff --git a/components/workflows/index.qmd b/components/workflows/index.qmd
@@ -0,0 +1,20 @@
+---
+title: "Workflows"
+description: An overview of the workflows in OpenPipelines
+order: 40
+listing:
+  - id: workflows
+    type: table
+    contents: "**.qmd"
+    fields: [title, namespace, description]
+    field-display-names: 
+        title: Name
+        namespace: Namespace
+        description: Description
+---
+
+
+## Workflows
+
+:::{#workflows}
+:::
diff --git a/fundamentals/architecture.qmd b/fundamentals/architecture.qmd
@@ -15,6 +15,100 @@ flowchart TD
   ingest["Ingestion"] --> split --> unimodalsinglesample["Unimodal Single Sample Processing"] --> concat --> unimodalmultisample["Unimodal Multi Sample Processing"] --> merging --> integation_setup["Integration Setup"] --> integration["Integration"]  --> downstreamprocessing["Downstream Processing"]
 ```
 
+```{mermaid}
+flowchart TB
+  subgraph ingestion
+    direction TB
+    subgraph cellranger_multi
+      direction TB
+      mapping_10x --> convert_to_h5mu_10x
+      mapping_10x[mapping]
+      convert_to_h5mu_10x[convert_to_h5mu]
+    end
+    subgraph bdrhap_v1
+      direction TB
+      mapping_bd1 --> convert_to_h5mu_bd1
+      mapping_bd1[mapping]
+      convert_to_h5mu_bd1[convert_to_h5mu]
+    end
+    subgraph bdrhap_v2
+      direction TB
+      mapping_bd2 --> convert_to_h5mu_bd2
+      mapping_bd2[mapping]
+      convert_to_h5mu_bd2[convert_to_h5mu]
+    end
+    cellranger_multi:::subwf
+    bdrhap_v1:::subwf
+    bdrhap_v2:::subwf
+  end
+  ingestion:::wf
+  subgraph process_samples
+    split_modalities --> rna_singlesample & prot_singlesample & gdo_singlesample & atac_singlesample & other_modalities --> concat --> process_batches
+    split_modalities
+    rna_singlesample
+    prot_singlesample
+    gdo_singlesample
+    atac_singlesample
+    other_modalities
+    concat
+    subgraph process_batches
+      direction LR
+      split_modalities2 --> rna_multisample & prot_multisample & atac_multisample & other_modalities2 --> merge
+      split_modalities2[split_modalities]
+      other_modalities2[other_modalities]
+      rna_multisample
+      prot_multisample
+      merge
+    end
+    process_batches:::subwf
+    atac_multisample
+  end
+  process_samples:::wf
+  raw_counts --- ingestion --> raw_h5mu
+  raw_h5mu --- process_samples --> processed_h5mu
+  subgraph integration
+    direction LR
+    integration_method --> find_neighbors --> leiden --> umap
+    integration_method -.- intmeth
+    integration_method
+    find_neighbors
+    leiden
+    umap
+    subgraph intmeth [integration_method]
+      bbknn
+      harmony
+      scanorama
+      scvi
+      totalvi
+      scgpt_integration
+    end
+    intmeth:::info
+  end
+  integration:::wf
+  processed_h5mu --- integration ---> integrated_h5mu
+  subgraph celltype_annotation
+    direction TB
+    integration_method2[integration_method]
+    celltypist
+    scanvi
+    scgpt_annotation
+    onclass
+    svm
+    randomforest
+    pynndescent_knn
+    consensus_voting
+    integration_method2 --> pynndescent_knn --> consensus_voting
+    celltypist & scanvi & scgpt_annotation & onclass & svm & randomforest --> consensus_voting
+  end
+  reference_atlas --> celltype_annotation
+  celltype_annotation:::wf
+  integrated_h5mu --- celltype_annotation --> annotated_h5mu
+
+  classDef wf fill:#f0f0f0,stroke:#525252
+  classDef subwf fill:#d9d9d9,stroke:#525252
+  classDef info fill:#f0f0f0,stroke:#525252,stroke-dasharray: 4 4
+```
+
 1. [Ingestion](#ingestion): Convert raw sequencing data or count tables into MuData data for further processing.
 2. [Splitting modalities](#sec-splitting): Creating several MuData objects, one per modality, out of a multimodal input sample.
 3. [Unimodal Single Sample Processing](#sec-single-sample): tools applied to each modality of samples individually. Mostly involves the selection of true from false cells.

diff --git a/fundamentals/roadmap.qmd b/fundamentals/roadmap.qmd
@@ -25,4 +25,115 @@ flowchart LR
   ProcGEX & ProcRNAV & ProcADT & ProcATAC & ProcVDJ --> Merge[/Merge\nmodalities/]:::done --> SetupIntegration[/Setup\nintegration/]:::done --> Integration[/Integration/]:::done
 ```
 
+:::
+
+
+:::{.column-screen-inset-shaded}
+```{mermaid}
+%%| label: fig-status2
+
+
+flowchart TB
+  subgraph ingestion
+    direction TB
+    subgraph cellranger_multi
+      direction TB
+      mapping_10x --> convert_to_h5mu_10x
+      mapping_10x[mapping]:::done
+      convert_to_h5mu_10x[convert_to_h5mu]:::done
+    end
+    subgraph bdrhap_v1
+      direction TB
+      mapping_bd1 --> convert_to_h5mu_bd1
+      mapping_bd1[mapping]:::done
+      convert_to_h5mu_bd1[convert_to_h5mu]:::done
+    end
+    subgraph bdrhap_v2
+      direction TB
+      mapping_bd2 --> convert_to_h5mu_bd2
+      mapping_bd2[mapping]:::wip
+      convert_to_h5mu_bd2[convert_to_h5mu]:::wip
+    end
+    cellranger_multi:::subwf
+    bdrhap_v1:::subwf
+    bdrhap_v2:::subwf
+  end
+  ingestion:::wf
+  subgraph process_samples
+    split_modalities --> rna_singlesample & prot_singlesample & gdo_singlesample & atac_singlesample & other_modalities --> concat --> process_batches
+    split_modalities:::done
+    rna_singlesample:::done
+    prot_singlesample:::done
+    gdo_singlesample:::done
+    atac_singlesample:::todo
+    other_modalities:::done
+    concat:::done
+    subgraph process_batches
+      direction LR
+      split_modalities2 --> rna_multisample & prot_multisample & atac_multisample & other_modalities2 --> merge
+      split_modalities2[split_modalities]:::done
+      other_modalities2[other_modalities]:::done
+      rna_multisample:::done
+      prot_multisample:::done
+      merge:::done
+    end
+    process_batches:::subwf
+    atac_multisample:::todo
+  end
+  process_samples:::wf
+  raw_counts --- ingestion --> raw_h5mu
+  raw_h5mu --- process_samples --> processed_h5mu
+  subgraph integration
+    direction LR
+    integration_method --> find_neighbors --> leiden --> umap
+    integration_method -.- intmeth
+    integration_method:::done
+    find_neighbors:::done
+    leiden:::done
+    umap:::done
+    subgraph intmeth [integration_method]
+      bbknn:::done
+      harmony:::done
+      scanorama:::done
+      scvi:::done
+      totalvi:::done
+      scgpt_integration:::wip
+    end
+    intmeth:::info
+  end
+  integration:::wf
+  processed_h5mu --- integration ---> integrated_h5mu
+  subgraph celltype_annotation
+    direction TB
+    integration_method2[integration_method]:::done
+    celltypist:::wip
+    scanvi:::wip
+    scgpt_annotation:::wip
+    onclass:::todo
+    svm:::todo
+    randomforest:::todo
+    pynndescent_knn:::wip
+    consensus_voting:::todo
+    integration_method2 --> pynndescent_knn --> consensus_voting
+    celltypist & scanvi & scgpt_annotation & onclass & svm & randomforest --> consensus_voting
+  end
+  reference_atlas --> celltype_annotation
+  celltype_annotation:::wf
+  integrated_h5mu --- celltype_annotation --> annotated_h5mu
+
+  classDef done fill:#ccebc5,stroke:#4daf4a
+  classDef wip fill:#fed9a6,stroke:#ff7f00
+  classDef todo fill:#fbb4ae,stroke:#e41a1c
+  classDef wf fill:#f0f0f0,stroke:#525252
+  classDef subwf fill:#d9d9d9,stroke:#525252
+  classDef info fill:#f0f0f0,stroke:#525252,stroke-dasharray: 4 4
+  
+  subgraph Legend
+    done[Done]:::done
+    wip[Work in progress]:::wip
+    todo[To do]:::todo
+  end
+  Legend:::info
+```
+
 :::
diff --git a/team/elizabeth_mlynarski/index.qmd b/team/elizabeth_mlynarski/index.qmd
@@ -0,0 +1,12 @@
+---
+title: Elizabeth Mlynarski
+image: /images/avatar.svg
+role: Contributor
+organizations:
+- name: Janssen R&D US
+  role: Principal Scientist Computational Genomics
+links: []
+about:
+  template: jolla
+---
+
diff --git a/team/kai_waldrant/index.qmd b/team/kai_waldrant/index.qmd
@@ -5,14 +5,23 @@ role: Contributor
 organizations:
 - name: Data Intuitive
   href: https://www.data-intuitive.com
-  role: Bioinformatics Workflow Developer
+  role: Bioinformatician
+- name: Open Problems
+  href: https://openproblems.bio
+  role: Contributor
 links:
+- icon: bi-envelope
+  text: E-mail
+  href: mailto:[email protected]
 - icon: bi-github
   text: GitHub
   href: https://github.com/KaiWaldrant
+- icon: fa-brands fa-orcid
+  text: ORCID
+  href: https://orcid.org/0009-0003-8555-1361
 - icon: bi-linkedin
   text: LinkedIn
-  href: https://www.linkedin.com/in/kai-waldrant-b8b86160
+  href: https://www.linkedin.com/in/kaiwaldrant
 about:
   template: jolla
 ---

diff --git a/team/weiwei_schultz/index.qmd b/team/weiwei_schultz/index.qmd
@@ -0,0 +1,12 @@
+---
+title: Weiwei Schultz
+image: /images/avatar.svg
+role: Contributor
+organizations:
+- name: Janssen R&D US
+  role: Associate Director Data Sciences
+links: []
+about:
+  template: jolla
+---
+
diff --git a/user_guide/index.qmd b/user_guide/index.qmd
@@ -1,5 +1,5 @@
 ---
-title: User Guide
+title: User guide
 sidebar: true
 listing:
   template: ../templates/listing.ejs