From b70ecc6b7667db653ad1923d383866d2f0661141 Mon Sep 17 00:00:00 2001 From: Nirmayi Date: Tue, 2 Jul 2024 09:26:14 +0200 Subject: [PATCH] update readme --- README.md | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 40c7287..9ddb773 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ Estimation of cell type proportions per spot in 2D space from spatial transcriptomic data coupled with corresponding single-cell data Path to source: -[`src`](https://github.com/openproblems-bio/task-spatial-decomposition/tree/main/src) +[`src`](https://github.com/openproblems-bio/task_spatial_decomposition/src) ## Motivation @@ -83,7 +83,7 @@ flowchart LR A subset of the common dataset. Example file: -`resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/dataset_simulated.h5ad` +`resources_test/common/cxg_mouse_pancreas_atlas/dataset.h5ad` Format: @@ -92,7 +92,7 @@ Format: AnnData object obs: 'cell_type', 'batch' var: 'hvg', 'hvg_score' - obsm: 'X_pca', 'coordinates', 'proportions_true' + obsm: 'X_pca' layers: 'counts' uns: 'cell_type_names', 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism' @@ -108,9 +108,7 @@ Slot description: | `obs["batch"]` | `string` | A batch identifier. This label is very context-dependent and may be a combination of the tissue, assay, donor, etc. | | `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | | `var["hvg_score"]` | `double` | A ranking of the features by hvg. | -| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | -| `obsm["coordinates"]` | `double` | (*Optional*) XY coordinates for each spot. | -| `obsm["proportions_true"]` | `double` | (*Optional*) True cell type proportions for each spot. | +| `obsm["X_pca"]` | `double` | (*Optional*) The resulting PCA embedding. | | `layers["counts"]` | `integer` | Raw counts. | | `uns["cell_type_names"]` | `string` | (*Optional*) Cell type names corresponding to values in `cell_type`. | | `uns["dataset_id"]` | `string` | A unique identifier for the dataset. |