clustering yaml creayed

docs/yaml_docs/index.rst

@@ -11,4 +11,5 @@ Workflows configuration files
     pipeline_clustering_yml
     spatial_qc
     spatial_preprocess
-    spatial_deconvolution
+    spatial_deconvolution
+    pipeline_clustering_yml.md

docs/yaml_docs/pipeline_clustering_yml.md

@@ -62,24 +62,29 @@ Prefix for the sample that comes out of the filtering/ preprocessing steps of th
   Specify the full object if your scaled_obj contains only HVG.  If your scaled_obj contains all the genes then leave full_obj blank. 
   panpipes will use the full object to do marker genes analysis (rank_gene_groups) and for plotting those genes. 
 - <span class="parameter">modalities</span><br>
-  - <span class="parameter">rna</span> `Boolean`, Default: True<br>
+ Which modalities to run clustering on. 
+  - <span class="parameter">rna</span> `Boolean`, Default: True<br> If set to `True`, the workflow will stop if it doesn't find a modality named 'rna'
   - <span class="parameter">prot</span> `Boolean`, Default: True<br>
+  If set to `True`, the workflow will stop if it doesn't find a modality named 'prot'
   - <span class="parameter">atac</span> `Boolean`, Default: False<br>
+   If set to `True`, the workflow will stop if it doesn't find a modality named 'atac'
+
   - <span class="parameter">spatial</span> `Boolean`, Default: False<br>
-  Run clustering on each individual modality.
+  If set to `True`, the workflow will stop if it doesn't find a modality named 'spatial'
+
 
 - <span class="parameter">multimodal</span><br>
-  - <span class="parameter">rna_clustering</span> `Boolean`, Default: True<br>
-  - <span class="parameter">integration_method</span> `String`, Default: WNN<br>
-  Options here include WNN, mofa, and totalVI, and it tells us where to look for.
+  - <span class="parameter">rna_clustering</span> `Boolean`, Default: False<br> If set to True, runs clustering on multimodal embedding
+  - <span class="parameter">integration_method</span> `String`, Default: None<br>
+  Specify the name of the multimodal embedding. Options here include WNN, mofa, totalvi, multivi. In case you have run WNN, the neigbhours calculation will be skipped since WNN provides its own.
 
 ## Parameters for finding neighbours 
 
 - <span class="parameter">neighbors:</span> 
  Sets the number of neighbors to use when calculating the graph for clustering and umap.
   - <span class="parameter">rna:</span> 
 
-     - <span class="parameter">use_existing </span> `Boolean`, Default: True<br>
+     - <span class="parameter">use_existing </span> `Boolean`, Default: True<br> Use existing neighbours in .uns calculated in the `integration` workflow. If `False`, it will recalculate using the following parameters
      - <span class="parameter">dim_red </span> `String`, Default: X_pca<br>
        Defines which representation in .obsm to use for nearest neighbors
      - <span class="parameter">n_dim_red</span> `Integer`, Default: 30<br>
@@ -94,7 +99,7 @@ Prefix for the sample that comes out of the filtering/ preprocessing steps of th
 
   - <span class="parameter">prot:</span> 
 
-     - <span class="parameter">use_existing </span> `Boolean`, Default: True<br>
+     - <span class="parameter">use_existing </span> `Boolean`, Default: True<br> Use existing neighbours in .uns calculated in the `integration` workflow. If `False`, it will recalculate using the following parameters
      - <span class="parameter">dim_red </span> `String`, Default: X_pca<br>
        Defines which representation in .obsm to use for nearest neighbors
      - <span class="parameter">n_dim_red</span> `Integer`, Default: 30<br>
@@ -109,7 +114,7 @@ Prefix for the sample that comes out of the filtering/ preprocessing steps of th
 
   - <span class="parameter">atac:</span> 
 
-     - <span class="parameter">use_existing </span> `Boolean`, Default: True<br>
+     - <span class="parameter">use_existing </span> `Boolean`, Default: True<br> Use existing neighbours in .uns calculated in the `integration` workflow. If `False`, it will recalculate using the following parameters
      - <span class="parameter">dim_red </span> `String`, Default: X_lsi<br>
        Defines which representation in .obsm to use for nearest neighbors
      - <span class="parameter">n_dim_red</span> `Integer`, Default: 1<br>
@@ -125,7 +130,7 @@ Prefix for the sample that comes out of the filtering/ preprocessing steps of th
 
   - <span class="parameter">spatial:</span> 
 
-     - <span class="parameter">use_existing </span> `Boolean`, Default: False<br>
+     - <span class="parameter">use_existing </span> `Boolean`, Default: False<br> Use existing neighbours in .uns calculated in the `integration` workflow. If `False`, it will recalculate using the following parameters
      - <span class="parameter">dim_red </span> `String`, Default: X_pca<br>
        Defines which representation in .obsm to use for nearest neighbors
      - <span class="parameter">n_dim_red</span> `Integer`, Default: 30<br>
@@ -142,7 +147,7 @@ Prefix for the sample that comes out of the filtering/ preprocessing steps of th
 
   - <span class="parameter">umap:</span> 
 
-     - <span class="parameter">run </span> `Boolean`, Default: True<br>
+     - <span class="parameter">run </span> `Boolean`, Default: True<br> Set to `True` runs the umap calculation and plotting.
      - <span class="parameter">rna:</span>
          - <span class="parameter">mindist </span> `Float`, Default: 0.5<br>
            Can specify an array: 0.25,0.5
@@ -265,7 +270,7 @@ When pseudo_seurat is set to True then a [python implementation](https://github.
    - <span class="parameter">threshuse </span> `Float`, Default: 0.25<br>
        This parameter is mandatory if pseudo_seurat is set to True 
 ## Plot specifications
-Used to define which metadata columns are used in the visualizations 
+Define which layers are used in the markers visualization 
  - <span class="parameter">plotspecs:</span><br>
    - <span class="parameter">layers: </span><br>
      - <span class="parameter">rna </span> `String`, Default: logged_counts<br>

panpipes/panpipes/pipeline_clustering/pipeline.yml

@@ -29,7 +29,7 @@ modalities:
   atac: False
   spatial: False
 
-# if True, will look for WNN, or totalVI output
+# if True, will look for WNN, mofa, multivi, totalVI embeddings
 multimodal:
   run_clustering: True
   integration_method: 
@@ -40,22 +40,26 @@ multimodal:
 # ---------------------------------------
 # 
 # -----------------------------
+
 neighbors:
   rna:
+    #use the knn calculated in the integration workflow. If False it will recalculate
     use_existing: True
     dim_red: X_pca
     n_dim_red: 30
     k: 30
     metric: euclidean
     method: scanpy
   prot:
+    #use the knn calculated in the integration workflow. If False it will recalculate
     use_existing: True
     dim_red: X_pca
     n_dim_red: 30
     k: 30
     metric: euclidean
     method: scanpy
   atac:
+    #use the knn calculated in the integration workflow. If False it will recalculate
     use_existing: True
     dim_red: X_lsi
     dim_remove: 1
@@ -64,6 +68,7 @@ neighbors:
     metric: euclidean
     method: scanpy
   spatial:
+    #use the knn calculated in the integration workflow. If False it will recalculate
     use_existing: False
     dim_red: X_pca
     n_dim_red: 30

panpipes/python_scripts/run_umap.py

@@ -33,7 +33,7 @@
                     default=0.1, 
                     help="no. neighbours parameters for sc.pp.neighbors()")
 parser.add_argument("--neighbors_key", 
-                    default="neighbors", help="algortihm choice from louvain and leiden")
+                    default="neighbors", help="name of the saved knn neighbors")
 
 args, opt = parser.parse_known_args()
 L.info(args)