Merge branch 'main' into sarah_spatial_actions

.github/workflows/spatial_ingestion_visium-ci.yml

@@ -0,0 +1,111 @@
+name: Run tutorials (spatial ingest visium)
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+env:
+  debug: 'true'
+
+jobs:
+  spatial_ingest_visium:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest"] # , "macos-latest", "windows-latest"
+        python-version: ["3.10"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: File tree
+        if: env.debug == 'true'
+        run: tree
+
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-version: latest
+          auto-activate-base: true
+          auto-update-conda: true
+          channels: conda-forge
+          channel-priority: strict
+          activate-environment: pipeline_env
+          environment-file: pipeline_env.yaml
+
+      - name: Install Panpipes
+        shell: bash -el {0}
+        run: |
+          pip install .[spatial]
+          conda list
+
+      - name: Conda info
+        if: env.debug == 'true'
+        shell: bash -el {0}
+        run: conda info
+
+      - name: Conda list
+        if: env.debug == 'true'
+        shell: pwsh
+        run: conda list
+
+
+      - name: Preparing the data
+        run: |
+          mkdir spatial spatial/ingestion spatial/ingestion/data
+          cd spatial/ingestion/data 
+          mkdir V1_Human_Heart V1_Human_Lymph_Node
+          cd V1_Human_Heart
+          curl -O https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Human_Heart/V1_Human_Heart_filtered_feature_bc_matrix.h5
+          curl -O https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Human_Heart/V1_Human_Heart_spatial.tar.gz
+          tar -xf V1_Human_Heart_spatial.tar.gz
+          cd ../V1_Human_Lymph_Node
+          curl -O https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Human_Lymph_Node/V1_Human_Lymph_Node_filtered_feature_bc_matrix.h5
+          curl -O https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Human_Lymph_Node/V1_Human_Lymph_Node_spatial.tar.gz
+          tar -xf V1_Human_Lymph_Node_spatial.tar.gz
+
+      # Note: we run the following to test that the commands works
+      - name: Preparing the configuration file
+        shell: bash -el {0}
+        run: |
+          cd spatial/ingestion
+          panpipes qc_spatial config
+
+      - name: Preparing the submission file
+        run: |
+          cd spatial/ingestion
+          curl -o sample_file_qc_spatial.txt https://raw.githubusercontent.com/DendrouLab/panpipes-tutorials/main/docs/ingesting_visium_data/sample_file_qc_spatial.txt
+
+      - name: Preparing the yaml file
+        run: |
+          cd spatial/ingestion
+          curl -o pipeline.yml https://raw.githubusercontent.com/DendrouLab/panpipes-tutorials/main/docs/ingesting_visium_data/pipeline.yml
+
+      - name: Replace template contents in configuration file
+        run: |
+          cd spatial/ingestion
+          sed -i 's+condaenv:+conda_env: pipeline_env+g' pipeline.yml
+
+      - name: File tree
+        if: env.debug == 'true'
+        run: tree spatial/ingestion
+
+      - name: Review pipeline tasks
+        shell: bash -el {0}
+        run: |
+          cd spatial/ingestion
+          panpipes qc_spatial show full --local
+
+      - name: Run pipeline tasks
+        shell: bash -el {0}
+        run: |
+          cd spatial/ingestion
+          panpipes qc_spatial make full --local
+
+      - name: File tree
+        if: env.debug == 'true'
+        run: tree spatial/ingestion

docs/usage/normalization_methods.md

@@ -18,6 +18,8 @@ Additionally, the normalized data can be scaled using scanpy's [sc.pp.scale](htt
 
     *if you come from R, please note that the [margins are transposed](https://images.hindustantimes.com/rf/image_size_630x354/HT/p2/2017/09/21/Pictures/_78c6a162-9e94-11e7-9c3b-8e901839ece0.JPG) in the Python and anndata world*
 
+   <img src="https://github.com/DendrouLab/panpipes/tree/main/docs/img/clr_margins.png" width="65%">
+
 2. dsb using [muon's prot processing](https://muon.readthedocs.io/en/latest/api/generated/muon.prot.pp.html). This method is only applicable when you have raw 10x inputs (see [supported input files](https://panpipes-pipelines.readthedocs.io/en/latest/usage/setup_for_qc_mm.html#supported-input-filetypes)).
 
 ## ATAC