Mercurial > repos > goeckslab > gate_finder

annotate vitessce_spatial.py @ 0:6df8d6e42152 draft

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
author goeckslab
date Thu, 08 Sep 2022 17:22:53 +0000
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6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
goeckslab
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diff changeset
1 import argparse
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
goeckslab
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2 import json
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
goeckslab
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3 import warnings
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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4 from pathlib import Path
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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5
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6 import scanpy as sc
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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7 from anndata import read_h5ad
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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8 from vitessce import (
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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9 AnnDataWrapper,
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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10 Component as cm,
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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11 MultiImageWrapper,
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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12 OmeTiffWrapper,
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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13 VitessceConfig,
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14 )
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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16
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17 def main(inputs, output, image, anndata=None, masks=None):
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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18 """
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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19 Parameter
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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20 ---------
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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21 inputs : str
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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22 File path to galaxy tool parameter.
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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23 output : str
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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24 Output folder for saving web content.
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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25 image : str
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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26 File path to the OME Tiff image.
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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27 anndata : str
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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28 File path to anndata containing phenotyping info.
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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29 masks : str
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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30 File path to the image masks.
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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31 """
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32 warnings.simplefilter('ignore')
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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33
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34 with open(inputs, 'r') as param_handler:
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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35 params = json.load(param_handler)
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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36
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37 vc = VitessceConfig(name=None, description=None)
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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38 dataset = vc.add_dataset()
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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39 image_wrappers = [OmeTiffWrapper(img_path=image, name='OMETIFF')]
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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40 if masks:
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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41 image_wrappers.append(
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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42 OmeTiffWrapper(img_path=masks, name='MASKS', is_bitmask=True)
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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43 )
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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44 dataset.add_object(MultiImageWrapper(image_wrappers))
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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45
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46 status = vc.add_view(dataset, cm.STATUS)
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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47 spatial = vc.add_view(dataset, cm.SPATIAL)
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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48 lc = vc.add_view(dataset, cm.LAYER_CONTROLLER)
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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49
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50 if not anndata:
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51 vc.layout(status / lc | spatial)
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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52 config_dict = vc.export(to='files', base_url='http://localhost', out_dir=output)
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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53 with open(Path(output).joinpath('config.json'), 'w') as f:
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54 json.dump(config_dict, f, indent=4)
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55 return
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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56
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57 adata = read_h5ad(anndata)
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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58
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59 params = params['do_phenotyping']
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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60 embedding = params['scatterplot_embeddings']['embedding']
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61 embedding_options = params['scatterplot_embeddings']['options']
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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62 if embedding == 'umap':
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63 sc.pp.neighbors(adata, **embedding_options)
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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64 sc.tl.umap(adata)
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65 mappings_obsm = 'X_umap'
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66 mappings_obsm_name = "UMAP"
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67 elif embedding == 'tsne':
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68 sc.tl.tsne(adata, **embedding_options)
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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69 mappings_obsm = 'X_tsne'
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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70 mappings_obsm_name = "tSNE"
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71 else: # pca
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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72 sc.tl.pca(adata, **embedding_options)
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73 mappings_obsm = 'X_pca'
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74 mappings_obsm_name = "PCA"
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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75
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76 adata.obsm['XY_centroid'] = adata.obs[['X_centroid', 'Y_centroid']].values
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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77
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78 cell_set_obs = params['phenotype_factory']['phenotypes']
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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79 if not isinstance(cell_set_obs, list):
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80 cell_set_obs = [x.strip() for x in cell_set_obs.split(',')]
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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81 cell_set_obs_names = [obj[0].upper() + obj[1:] for obj in cell_set_obs]
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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82 dataset.add_object(
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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83 AnnDataWrapper(
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84 adata,
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85 mappings_obsm=[mappings_obsm],
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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86 mappings_obsm_names=[mappings_obsm_name],
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87 spatial_centroid_obsm='XY_centroid',
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88 cell_set_obs=cell_set_obs,
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89 cell_set_obs_names=cell_set_obs_names,
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90 expression_matrix="X"
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91 )
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92 )
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93
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94 cellsets = vc.add_view(dataset, cm.CELL_SETS)
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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95 scattorplot = vc.add_view(dataset, cm.SCATTERPLOT, mapping=mappings_obsm_name)
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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96 heatmap = vc.add_view(dataset, cm.HEATMAP)
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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97 genes = vc.add_view(dataset, cm.GENES)
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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98 cell_set_sizes = vc.add_view(dataset, cm.CELL_SET_SIZES)
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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99 cell_set_expression = vc.add_view(dataset, cm.CELL_SET_EXPRESSION)
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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100 vc.layout(
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101 (status / genes / cell_set_expression)
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102 | (cellsets / lc / scattorplot)
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103 | (cell_set_sizes / heatmap / spatial)
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104 )
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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105 config_dict = vc.export(to='files', base_url='http://localhost', out_dir=output)
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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106
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107 with open(Path(output).joinpath('config.json'), 'w') as f:
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108 json.dump(config_dict, f, indent=4)
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109
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110
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111 if __name__ == '__main__':
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112 aparser = argparse.ArgumentParser()
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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113 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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114 aparser.add_argument("-e", "--output", dest="output", required=True)
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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115 aparser.add_argument("-g", "--image", dest="image", required=True)
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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116 aparser.add_argument("-a", "--anndata", dest="anndata", required=False)
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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117 aparser.add_argument("-m", "--masks", dest="masks", required=False)
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118
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119 args = aparser.parse_args()
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120
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121 main(args.inputs, args.output, args.image, args.anndata, args.masks)