diff --git a/openapi/v1/integrationCurator.yaml b/openapi/v1/integrationCurator.yaml index aa54ab76..5173adbd 100644 --- a/openapi/v1/integrationCurator.yaml +++ b/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. diff --git a/openapi/v1/integrationUser.yaml b/openapi/v1/integrationUser.yaml index d38b6c30..0ea9ca11 100644 --- a/openapi/v1/integrationUser.yaml +++ b/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. diff --git a/openapi/v1/job.yaml b/openapi/v1/job.yaml index fae50862..ab6538e3 100644 --- a/openapi/v1/job.yaml +++ b/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**. diff --git a/openapi/v1/schemas/cell/Cell.yaml b/openapi/v1/schemas/cell/Cell.yaml index 25e67dd1..4d636509 100644 --- a/openapi/v1/schemas/cell/Cell.yaml +++ b/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" diff --git a/openapi/v1/schemas/cell/CellListResponse.yaml b/openapi/v1/schemas/cell/CellListResponse.yaml index 6829ee88..996e840e 100644 --- a/openapi/v1/schemas/cell/CellListResponse.yaml +++ b/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"