[ODM-12914] Support t-sne parameter in cell metadata.

openapi/v1/integrationCurator.yaml

@@ -4488,13 +4488,13 @@ paths:
             1. Strings: `barcode`, `batch`, `cellType`, `cluster`, and all custom attributes.
             2. Integers: `nCounts`
             3. Floats: `percentMito`
-            4. Float coordinates: `UMAP`, `PCA`.
+            4. Float coordinates: `UMAP`, `PCA`, `t-SNE`.
             5. All other attributes are considered to be custom and stored as string data type.
 
             To use filters for cell metadata objects use the following query types:
             1. By key=value pair for attributes. Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace: `cellType=T_cell`, `batch="PBMC batch 01"` - quote values that include spaces, `nCounts=3000`, `custom_attribute="disease"` - custom attribute with string data type.
             2. It is possible to specify a set of possible values, separated by comma: `cellType=Macrophage,Monocyte`.
-            3. Utilize range filters to search numeric attributes. Apply `<` (less than), `>` (greater than), and `=` (equal to) symbols to specify the desired ranges as follows: `nCounts > 2000`, `-3 < percentMito < 10`. To retrieve UMAP or PCA values use `umap.1`, `umap.2`, `pca.1`, `pca.2`, e.g. `umap.1 > 0.5`.
+            3. Utilize range filters to search numeric attributes. Apply `<` (less than), `>` (greater than), and `=` (equal to) symbols to specify the desired ranges as follows: `nCounts > 2000`, `-3 < percentMito < 10`. To retrieve UMAP, PCA or t-SNE values use `umap.1`, `umap.2`, `pca.1`, `pca.2`, `tsne.1`, `tsne.2`, e.g. `umap.1 > 0.5`.
             4. Use substring search to get the records where the attribute field contains the provided substring: `cellType =~ "B cell"`.
             5. Combine multiple filters for different feature attributes and measurements using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses:
             * `NOT cellType=Erythrocyte` or `cellType!=B_cell,T_cell`: exclude objects with defined values from search.
@@ -4677,13 +4677,13 @@ paths:
             1. Strings: `barcode`, `batch`, `cellType`, `cluster`, and all custom attributes.
             2. Integers: `nCounts`
             3. Floats: `percentMito`
-            4. Float coordinates: `UMAP`, `PCA`.
+            4. Float coordinates: `UMAP`, `PCA`, `t-SNE`.
             5. All other attributes are considered to be custom and stored as string data type.
 
             To use filters for cell metadata objects use the following query types:
             1. By key=value pair for attributes. Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace: `cellType=T_cell`, `batch="PBMC batch 01"` - quote values that include spaces, `nCounts=3000`, `custom_attribute="disease"` - custom attribute with string data type.
             2. It is possible to specify a set of possible values, separated by comma: `cellType=Macrophage,Monocyte`.
-            3. Utilize range filters to search numeric attributes. Apply `<` (less than), `>` (greater than), and `=` (equal to) symbols to specify the desired ranges as follows: `nCounts > 2000`, `-3 < percentMito < 10`. To retrieve UMAP or PCA values use `umap.1`, `umap.2`, `pca.1`, `pca.2`, e.g. `umap.1 > 0.5`.
+            3. Utilize range filters to search numeric attributes. Apply `<` (less than), `>` (greater than), and `=` (equal to) symbols to specify the desired ranges as follows: `nCounts > 2000`, `-3 < percentMito < 10`. To retrieve UMAP, PCA or t-SNE values use `umap.1`, `umap.2`, `pca.1`, `pca.2`, `tsne.1`, `tsne.2`, e.g. `umap.1 > 0.5`.
             4. Use substring search to get the records where the attribute field contains the provided substring: `cellType =~ "B cell"`.
             5. Combine multiple filters for different feature attributes and measurements using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses:
             * `NOT cellType=Erythrocyte` or `cellType!=B_cell,T_cell`: exclude objects with defined values from search.

openapi/v1/integrationUser.yaml

@@ -2935,13 +2935,13 @@ paths:
             1. Strings: `barcode`, `batch`, `cellType`, `cluster`, and all custom attributes.
             2. Integers: `nCounts`
             3. Floats: `percentMito`
-            4. Float coordinates: `UMAP`, `PCA`.
+            4. Float coordinates: `UMAP`, `PCA`, `t-SNE`.
             5. All other attributes are considered to be custom and stored as string data type.
 
             To use filters for cell metadata objects use the following query types:
             1. By key=value pair for attributes. Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace: `cellType=T_cell`, `batch="PBMC batch 01"` - quote values that include spaces, `nCounts=3000`, `custom_attribute="disease"` - custom attribute with string data type.
             2. It is possible to specify a set of possible values, separated by comma: `cellType=Macrophage,Monocyte`.
-            3. Utilize range filters to search numeric attributes. Apply `<` (less than), `>` (greater than), and `=` (equal to) symbols to specify the desired ranges as follows: `nCounts > 2000`, `-3 < percentMito < 10`. To retrieve UMAP or PCA values use `umap.1`, `umap.2`, `pca.1`, `pca.2`, e.g. `umap.1 > 0.5`.
+            3. Utilize range filters to search numeric attributes. Apply `<` (less than), `>` (greater than), and `=` (equal to) symbols to specify the desired ranges as follows: `nCounts > 2000`, `-3 < percentMito < 10`. To retrieve UMAP, PCA or t-SNE values use `umap.1`, `umap.2`, `pca.1`, `pca.2`, `tsne.1`, `tsne.2`, e.g. `umap.1 > 0.5`.
             4. Use substring search to get the records where the attribute field contains the provided substring: `cellType =~ "B cell"`.
             5. Combine multiple filters for different feature attributes and measurements using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses:
             * `NOT cellType=Erythrocyte` or `cellType!=B_cell,T_cell`: exclude objects with defined values from search.
@@ -3124,13 +3124,13 @@ paths:
             1. Strings: `barcode`, `batch`, `cellType`, `cluster`, and all custom attributes.
             2. Integers: `nCounts`
             3. Floats: `percentMito`
-            4. Float coordinates: `UMAP`, `PCA`.
+            4. Float coordinates: `UMAP`, `PCA`, `t-SNE`.
             5. All other attributes are considered to be custom and stored as string data type.
 
             To use filters for cell metadata objects use the following query types:
             1. By key=value pair for attributes. Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace: `cellType=T_cell`, `batch="PBMC batch 01"` - quote values that include spaces, `nCounts=3000`, `custom_attribute="disease"` - custom attribute with string data type.
             2. It is possible to specify a set of possible values, separated by comma: `cellType=Macrophage,Monocyte`.
-            3. Utilize range filters to search numeric attributes. Apply `<` (less than), `>` (greater than), and `=` (equal to) symbols to specify the desired ranges as follows: `nCounts > 2000`, `-3 < percentMito < 10`. To retrieve UMAP or PCA values use `umap.1`, `umap.2`, `pca.1`, `pca.2`, e.g. `umap.1 > 0.5`.
+            3. Utilize range filters to search numeric attributes. Apply `<` (less than), `>` (greater than), and `=` (equal to) symbols to specify the desired ranges as follows: `nCounts > 2000`, `-3 < percentMito < 10`. To retrieve UMAP, PCA or `t-SNE` values use `umap.1`, `umap.2`, `pca.1`, `pca.2`, `tsne.1`, `tsne.2`, e.g. `umap.1 > 0.5`.
             4. Use substring search to get the records where the attribute field contains the provided substring: `cellType =~ "B cell"`.
             5. Combine multiple filters for different feature attributes and measurements using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses:
             * `NOT cellType=Erythrocyte` or `cellType!=B_cell,T_cell`: exclude objects with defined values from search.

openapi/v1/job.yaml

@@ -311,10 +311,10 @@ paths:
 
         Embedding constraints:
 
-        * UMAP
+        * UMAP/t-SNE
           - Allowed number of dimensions per cell: **0** (absent) or **≥ 2**.
-          - If exactly **1** UMAP dimension is provided, the request is invalid.
-          - At most **3** UMAP dimensions are stored; if more than 3 are provided, only the first 3 are kept and the rest are ignored.
+          - If exactly **1** UMAP/t-SNE dimension is provided, the request is invalid.
+          - At most **3** UMAP/t-SNE dimensions are stored; if more than 3 are provided, only the first 3 are kept and the rest are ignored.
 
         * PCA
           - Allowed number of components per cell: **0** (absent) or **≥ 2**.
@@ -370,10 +370,10 @@ paths:
 
         Embedding constraints:
 
-        * UMAP
+        * UMAP/t-SNE
           - Allowed number of dimensions per cell: **0** (absent) or **≥ 2**.
-          - If exactly **1** UMAP dimension is provided, the request is invalid.
-          - At most **3** UMAP dimensions are stored; if more than 3 are provided, only the first 3 are kept and the rest are ignored.
+          - If exactly **1** UMAP/t-SNE dimension is provided, the request is invalid.
+          - At most **3** UMAP/t-SNE dimensions are stored; if more than 3 are provided, only the first 3 are kept and the rest are ignored.
 
         * PCA
           - Allowed number of components per cell: **0** (absent) or **≥ 2**.

openapi/v1/schemas/cell/Cell.yaml

@@ -13,8 +13,9 @@ description: |+
     - `cluster`: string - clustering labels, e.g. `leiden_res1`.
     - `nCounts`: integer - total UMI count (Unique Molecular Identifier), e.g. `1250`.
     - `percentMito`: number - percentage of mitochondrial gene expression, e.g. `5.2`.
-    - `umap`: array of two numbers - dimensionality reduction results (Uniform Manifold Approximation and Projection), e.g. `[1.23, 0.45]`.
-    - `pca`: array of two numbers - dimensionality reduction results (Principal Component Analysis results), e.g. `[0.12, 0.34]`.
+    - `umap`: array of two or three numbers - dimensionality reduction results (Uniform Manifold Approximation and Projection), e.g. `[1.23, 0.45]`.
+    - `pca`: array of between 2 and 100 numbers - dimensionality reduction results (Principal Component Analysis results), e.g. `[0.12, 0.34]`.
+    - `tsne`: array of two or three numbers - dimensionality reduction results (t-distributed Stochastic Neighbor Embedding), e.g. `[1.23, 0.45]`.
 
   **Dynamic:**
     - Any additional attributes in a form of key-value pairs, which can vary between different cell objects.
@@ -28,4 +29,5 @@ example:
   percentMito: 5.2
   umap: [1.23, 0.45]
   pca: [0.12, 0.34]
+  tsne: [1.23, 0.45]
   assay_custom: "10x 3' v2"

openapi/v1/schemas/cell/CellListResponse.yaml

@@ -22,6 +22,7 @@ example:
       percentMito: 5.2
       umap: [1.23, 0.45]
       pca: [0.12, 0.34]
+      tsne: [1.23, 0.45]
       assay_custom: "10x 3' v2"
     - cellId: "GSF222333-AAAGATGGTTCCTCCA-1"
       barcode: "AAAGATGGTTCCTCCA-1"