update fields

Author: rcannood

README.md

@@ -98,8 +98,8 @@ Data structure:
 | `obs["sample"]` | `string` | Sample ID. |
 | `obs["donor"]` | `string` | Donor ID. |
 | `obs["group"]` | `string` | Biological group of the donor. |
-| `obs["is_control"]` | `integer` | Whether the sample the cell came from can be used as a control for batch effect correction. 0: cannot be used as a control. \>= 1: can be used as a control. For cells with \>= 1: cells with the same value come from the same donor. Different values indicate different donors. |
-| `obs["split"]` | `integer` | Which split the cell will be used in. |
+| `obs["is_control"]` | `integer` | Whether the sample the cell came from can be used as a control for batch effect correction. \* 0: cannot be used as a control. \* \>= 1: can be used as a control. \* For cells with \>= 1: cells with the same value come from the same donor. Different values indicate different donors. |
+| `obs["split"]` | `integer` | Which split the cell will be used in. \* 0: control samples \* 1: split 1 (left) \* 2: split 2 (right) . |
 | `var["numeric_id"]` | `integer` | Numeric ID associated with each marker. |
 | `var["channel"]` | `string` | The channel / detector of the instrument. |
 | `var["marker"]` | `string` | (*Optional*) The marker name associated with the channel. |
@@ -174,7 +174,7 @@ Data structure:
 |:---|:---|:---|
 | `obs["batch"]` | `string` | Batch information. |
 | `obs["sample"]` | `string` | Sample ID. |
-| `obs["is_control"]` | `integer` | Whether the sample the cell came from can be used as a control for batch effect correction. 0: cannot be used as a control. \>= 1: can be used as a control. For cells with \>= 1: cells with the same value come from the same donor. Different values indicate different donors. |
+| `obs["is_control"]` | `integer` | Whether the sample the cell came from can be used as a control for batch effect correction. \* 0: cannot be used as a control. \* \>= 1: can be used as a control. \* For cells with \>= 1: cells with the same value come from the same donor. Different values indicate different donors. |
 | `var["numeric_id"]` | `integer` | Numeric ID associated with each marker. |
 | `var["channel"]` | `string` | The channel / detector of the instrument. |
 | `var["marker"]` | `string` | (*Optional*) The marker name associated with the channel. |
@@ -210,7 +210,7 @@ Format:
 <div class="small">
 
     AnnData object
-     obs: 'cell_type', 'batch', 'sample', 'donor', 'group', 'split'
+     obs: 'cell_type', 'batch', 'sample', 'donor', 'group', 'is_control', 'split'
      var: 'numeric_id', 'channel', 'marker', 'marker_type', 'to_correct'
      layers: 'preprocessed'
      uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'parameter_som_xdim', 'parameter_som_ydim', 'parameter_num_clusters'
@@ -228,7 +228,8 @@ Data structure:
 | `obs["sample"]` | `string` | Sample ID. |
 | `obs["donor"]` | `string` | Donor ID. |
 | `obs["group"]` | `string` | Biological group of the donor. |
-| `obs["split"]` | `integer` | Which split the cell will be used in. |
+| `obs["is_control"]` | `integer` | Whether the sample the cell came from can be used as a control for batch effect correction. \* 0: cannot be used as a control. \* \>= 1: can be used as a control. \* For cells with \>= 1: cells with the same value come from the same donor. Different values indicate different donors. |
+| `obs["split"]` | `integer` | Which split the cell will be used in. \* 0: control samples \* 1: split 1 (left) \* 2: split 2 (right) . |
 | `var["numeric_id"]` | `integer` | Numeric ID associated with each marker. |
 | `var["channel"]` | `string` | The channel / detector of the instrument. |
 | `var["marker"]` | `string` | (*Optional*) The marker name associated with the channel. |

src/api/file_censored.yaml

@@ -34,9 +34,11 @@ info:
         description: |
           Whether the sample the cell came from can be used as a control for batch 
           effect correction.
-          0: cannot be used as a control.
-          >= 1: can be used as a control.
-          For cells with >= 1: cells with the same value come from the same donor.
+          
+          * 0: cannot be used as a control.
+          * >= 1: can be used as a control.
+          * For cells with >= 1: cells with the same value come from the same donor.
+          
           Different values indicate different donors.
         required: true
     var:

src/api/file_common_dataset.yaml

@@ -45,6 +45,9 @@ info:
         name: split
         description: |
           Which split the cell will be used in.
+          0: control samples
+          1: split 1 (left)
+          2: split 2 (right)
         required: true
     var:
       - type: integer

src/api/file_unintegrated.yaml

@@ -38,10 +38,26 @@ info:
         name: group
         description: Biological group of the donor
         required: true
+      - type: integer
+        name: is_control
+        description: |
+          Whether the sample the cell came from can be used as a control for batch 
+          effect correction.
+          
+          * 0: cannot be used as a control.
+          * >= 1: can be used as a control.
+          * For cells with >= 1: cells with the same value come from the same donor.
+          
+          Different values indicate different donors.
+        required: true
       - type: integer
         name: split
         description: |
           Which split the cell will be used in.
+          
+          * 0: control samples
+          * 1: split 1 (left)
+          * 2: split 2 (right)
         required: true
     var:
       - type: integer