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Tang-Lab-super / PROST

PROST: A quantitative pattern recognition framework for spatial transcriptomics.
MIT License
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如何加入其他空间数据进行分析 #5

Closed JWJ13164328557 closed 3 months ago

JWJ13164328557 commented 4 months ago

我加入了我们自己的空间数据，添加了空间位置信息进去，保存成loom后转成h5ad格式导入流程，但报错

rootdir = '/data/liux/quanxibaohebingchulijiaoben/julei/ZCL/BSTViewer_project/jz/S_T1_1_all/SCT_C10_F50_P30_R0.5' input_dir = os.path.join(rootdir) output_dir = os.path.join(rootdir, 'results/') adata=sc.read(input_dir+"/object.h5ad") adata = PROST.prepare_for_PI(adata, percentage = 0.01, platform="/data/liux/quanxibaohebingchulijiaoben/julei/ZCL/BSTViewer_project/jz/S_T11all/SCT_C10_F50_P30_R0.5")

Filtering genes ... Traceback (most recent call last): File "", line 1, in File "/home/liux/miniconda3/envs/BMCstereoseq/PROST-1.1.2/PROST/calculate_PI.py", line 29, in prepare_for_PI locates = adata.obsm["spatial"].astype(float) File "/home/liux/miniconda3/envs/Genomic/lib/python3.9/site-packages/anndata/_core/aligned_mapping.py", line 196, in getitem return self._data[key] KeyError: 'spatial' 添加空间位置信息如下： AnnData object with n_obs × n_vars = 18367 × 34140 obs: 'Row.names', 'SCT_snn_res.0.5', 'nCount_RNA', 'nCount_SCT', 'nFeature_RNA', 'nFeature_SCT', 'orig.ident', 'pos_h', 'pos_w', 'seurat_clusters' layers: 'counts'

Sicrve11 commented 4 months ago

数据格式的问题，空间位置信息需要加到adata.obsm["spatial"]字段下面，可以根据你的空转平台去参考对应的示例数据。