Update README.md

README.md

@@ -6,6 +6,32 @@ Niche is the microenvironment in which each cell exists and is able to keep its
 
 The task is to predict niche type of each cell given spatial expression data (in total 6 types). The raw dataset is from [human liver sample](https://nanostring.com/products/cosmx-spatial-molecular-imager/ffpe-dataset/human-liver-rna-ffpe-dataset), including a healthy sample slide. We collected the data and randomly split the total set into train, valid and split.
 
+Each `.h5ad` file contains spatial coordinate information (`x`, `y`) and niche type (`niche_label`). The obs `niche` is exact name and `niche_label` is corresponding name index (this is input label column for running modelgenerator).
+
+```bash
+>>> import anndata as ad
+>>> file = 'niche_type_classification/cosmx_liver_for_celltype_niche.test.h5ad'
+>>> adata = ad.read_h5ad(file)
+>>> adata
+AnnData object with n_obs × n_vars = 34573 × 19264
+    obs: 'cellType', 'niche', 'split', 'x', 'y', 'cellType_label', 'niche_label'
+>>> adata.obs
+                              cellType    niche split         x        y cellType_label niche_label
+obs_id                                                                                             
+c_1_103_1                        Hep.5  Zone_2b  test  10.25828  9.73440              1           0
+c_1_103_10                       Hep.6  Zone_3a  test  10.61444  9.73356              7           2
+c_1_103_100                      Hep.1  Zone_3a  test  10.57556  9.67620              3           2
+c_1_103_1000                     Hep.5  Zone_2a  test  10.64528  9.24828              1           1
+c_1_103_1001                     Hep.4  Zone_2b  test  10.70828  9.24180              0           0
+...                                ...      ...   ...       ...      ...            ...         ...
+c_1_99_995                       Hep.5  Zone_2a  test   8.24356  9.31284              1           1
+c_1_99_996                       Hep.5  Zone_2b  test   8.28724  9.31428              1           0
+c_1_99_997                       Hep.4  Zone_2a  test   8.41696  9.31512              0           1
+c_1_99_998                       Hep.4  Zone_2b  test   8.57044  9.31524              0           0
+c_1_99_999    Inflammatory.macrophages  Zone_2a  test   8.25976  9.31596              9           1
+
+[34573 rows x 7 columns]
+```
 
 ## cell density
 
@@ -13,6 +39,32 @@ The task is to predict neighbor cell number of a target cell given the expressio
 
 The raw dataset is from [human liver sample](https://nanostring.com/products/cosmx-spatial-molecular-imager/ffpe-dataset/human-liver-rna-ffpe-dataset), including a healthy and tumor sample slide. We collected the data and curated ground truth neighbor number as in [Schaar et al.](https://www.biorxiv.org/content/10.1101/2024.04.15.589472v2). Then we randomly split the total set into train, valid and split.
 
+Each `.h5ad` file contains spatial coordinate information (`x`, `y`) and density value (`density`).
+
+```bash
+>>> file = 'cell_density/xenium_lung_for_density.test.h5ad'
+>>> adata = ad.read_h5ad(file)
+>>> adata
+AnnData object with n_obs × n_vars = 124058 × 19264
+    obs: 'density', 'split', 'x', 'y'
+>>> adata.obs
+              density split             x            y
+cell_id                                               
+aaaaaahk-1-0      7.0  test    497.832559   855.178702
+aaaandcd-1-0     21.0  test   1732.162622   856.926639
+aaabfmfn-1-0     21.0  test   1718.817560   853.211935
+aaabmojc-1-0     24.0  test   1724.924030   860.927252
+aaadaeog-1-0     19.0  test   2248.489685   862.145029
+...               ...   ...           ...          ...
+oilcikef-1-1      4.0  test  10815.658984  8476.788525
+oilfbafk-1-1      5.0  test  11116.310791  8524.649170
+oilfpbmk-1-1      6.0  test  11128.255615  8538.087305
+oilgfkkb-1-1      2.0  test  11051.862695  8556.525830
+oilgkofb-1-1      4.0  test  11085.344727  8522.173047
+
+[124058 rows x 4 columns]
+```
+
 ## other files
 
 `scRNA_genename_and_index.tsv`: gene name and index corresponds to .h5ad file