Mercurial > repos > iuc > anndata_manipulate
comparison manipulate.xml @ 10:9bd945a03d7b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 58ea92c594280588f6045093d77af6d7d885185d"
author | iuc |
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date | Sat, 07 May 2022 19:55:59 +0000 |
parents | b85871dd69f9 |
children | 3d748954434b |
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9:8db95f488f0f | 10:9bd945a03d7b |
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388 | 388 |
389 This tool takes a AnnData dataset, manipulates it and returns it. | 389 This tool takes a AnnData dataset, manipulates it and returns it. |
390 | 390 |
391 The possible manipulations are: | 391 The possible manipulations are: |
392 | 392 |
393 - Concatenate along the observations axis (`concatenate method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.concatenate.html>`__) | 393 - Concatenate along the observations axis (`concatenate method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.concatenate.html>`__) |
394 | 394 |
395 The `uns`, `varm` and `obsm` attributes are ignored. | 395 The `uns`, `varm` and `obsm` attributes are ignored. |
396 | 396 |
397 If you use `join='outer'` this fills 0s for sparse data when variables are absent in a batch. Use this with care. Dense data is filled with `NaN` | 397 If you use `join='outer'` this fills 0s for sparse data when variables are absent in a batch. Use this with care. Dense data is filled with `NaN` |
398 | 398 |
399 - Makes the obs index unique by appending '1', '2', etc (`obs_names_make_unique method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.obs_names_make_unique.html>`__) | 399 - Makes the obs index unique by appending '1', '2', etc (`obs_names_make_unique method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.obs_names_make_unique.html>`__) |
400 | 400 |
401 The first occurance of a non-unique value is ignored. | 401 The first occurance of a non-unique value is ignored. |
402 | 402 |
403 - Makes the var index unique by appending '1', '2', etc (`var_names_make_unique method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.var_names_make_unique.html>`__) | 403 - Makes the var index unique by appending '1', '2', etc (`var_names_make_unique method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.var_names_make_unique.html>`__) |
404 | 404 |
405 The first occurance of a non-unique value is ignored. | 405 The first occurance of a non-unique value is ignored. |
406 | 406 |
407 - Rename categories of annotation `key` in `obs`, `var` and `uns` (`rename_categories method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.rename_categories.html>`__) | 407 - Rename categories of annotation `key` in `obs`, `var` and `uns` (`rename_categories method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.rename_categories.html>`__) |
408 | 408 |
409 Besides calling `self.obs[key].cat.categories = categories` - similar for `var` - this also renames categories in unstructured annotation that uses the categorical annotation `key` | 409 Besides calling `self.obs[key].cat.categories = categories` - similar for `var` - this also renames categories in unstructured annotation that uses the categorical annotation `key` |
410 | 410 |
411 - Transform string annotations to categoricals (`strings_to_categoricals method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.strings_to_categoricals.html>`__) | 411 - Transform string annotations to categoricals (`strings_to_categoricals method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.strings_to_categoricals.html>`__) |
412 | 412 |
413 Only affects string annotations that lead to less categories than the total number of observations. | 413 Only affects string annotations that lead to less categories than the total number of observations. |
414 | 414 |
415 - Transpose the data matrix, leaving observations and variables interchanged (`transpose method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.transpose.html>`__) | 415 - Transpose the data matrix, leaving observations and variables interchanged (`transpose method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.transpose.html>`__) |
416 | 416 |
417 Data matrix is transposed, observations and variables are interchanged. | 417 Data matrix is transposed, observations and variables are interchanged. |
418 | 418 |
419 - Add annotation for variables or observations | 419 - Add annotation for variables or observations |
420 | 420 |