diff --git a/.buildinfo b/.buildinfo index 19428d9..d22f600 100644 --- a/.buildinfo +++ b/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 -# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: e077c98cfd0f535984f44fa35c53f65a +# This file records the configuration used when building these files. When it is not found, a full rebuild will be done. +config: c7a5e7534e8bed83617678857de0a551 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/_modules/index.html b/_modules/index.html index a002dd1..eaa3aa1 100644 --- a/_modules/index.html +++ b/_modules/index.html @@ -4,8 +4,8 @@ - - Overview: module code - MultiAssayExperiment 0.4.4 documentation + + Overview: module code - MultiAssayExperiment 0.5.0 documentation @@ -166,7 +166,7 @@
-
MultiAssayExperiment 0.4.4 documentation
 +
MultiAssayExperiment 0.5.0 documentation
@@ -190,7 +190,7 @@
- MultiAssayExperiment 0.4.4 documentation + MultiAssayExperiment 0.5.0 documentation
@@ -282,8 +282,8 @@

All modules for which code is available

-
- +
+ diff --git a/_modules/multiassayexperiment/MultiAssayExperiment.html b/_modules/multiassayexperiment/MultiAssayExperiment.html index b96fb99..79f0a9b 100644 --- a/_modules/multiassayexperiment/MultiAssayExperiment.html +++ b/_modules/multiassayexperiment/MultiAssayExperiment.html @@ -4,8 +4,8 @@ - - multiassayexperiment.MultiAssayExperiment - MultiAssayExperiment 0.4.4 documentation + + multiassayexperiment.MultiAssayExperiment - MultiAssayExperiment 0.5.0 documentation @@ -166,7 +166,7 @@
-
MultiAssayExperiment 0.4.4 documentation
 +
MultiAssayExperiment 0.5.0 documentation
@@ -190,7 +190,7 @@
- MultiAssayExperiment 0.4.4 documentation + MultiAssayExperiment 0.5.0 documentation @@ -303,9 +303,7 @@

Source code for multiassayexperiment.MultiAssayExperiment

_sample_set = set(_samples) _sample_diff = _sample_set.difference(column_data.row_names) if len(_sample_diff) > 0: - raise ValueError( - "`sample_map`'s 'primary' contains samples not represented by 'row_names' from `column_data`." - ) + raise ValueError("`sample_map`'s 'primary' contains samples not represented by 'row_names' from `column_data`.") if len(_sample_set) != column_data.shape[0]: warn("'primary' from `sample_map` & `column_data` mismatch.", UserWarning) @@ -316,9 +314,7 @@

Source code for multiassayexperiment.MultiAssayExperiment

smap_unique_assays = set(sample_map.get_column("assay")) unique_expt_names = set(list(experiments.keys())) - if (len(unique_expt_names) != len(smap_unique_assays)) or ( - unique_expt_names != smap_unique_assays - ): + if (len(unique_expt_names) != len(smap_unique_assays)) or (unique_expt_names != smap_unique_assays): warn( "'experiments' contains names not represented in 'sample_map' or vice-versa.", UserWarning, @@ -334,9 +330,7 @@

Source code for multiassayexperiment.MultiAssayExperiment

) if set(rows.get_column("colname")) != set(experiments[grp].column_names): - raise ValueError( - f"Experiment '{grp}' does not contain all columns mentioned in `sample_map`." - ) + raise ValueError(f"Experiment '{grp}' does not contain all columns mentioned in `sample_map`.") def _validate_sample_map(sample_map, column_data, experiments): @@ -347,9 +341,7 @@

Source code for multiassayexperiment.MultiAssayExperiment

raise TypeError("'sample_map' is not a `BiocFrame` object.") if not set(["assay", "primary", "colname"]).issubset(sample_map.column_names): - raise ValueError( - "'sample_map' does not contain required columns: 'assay', 'primary' and 'colname'." - ) + raise ValueError("'sample_map' does not contain required columns: 'assay', 'primary' and 'colname'.") _validate_column_data(column_data) _validate_sample_map_with_column_data(sample_map, column_data) @@ -371,9 +363,7 @@

Source code for multiassayexperiment.MultiAssayExperiment

samples.append(asy_sample) - sample_map = biocframe.BiocFrame( - {"assay": _all_assays, "primary": _all_primary, "colname": _all_colnames} - ) + sample_map = biocframe.BiocFrame({"assay": _all_assays, "primary": _all_primary, "colname": _all_colnames}) col_data = biocframe.BiocFrame({"samples": samples}, row_names=samples) return col_data, sample_map @@ -465,9 +455,7 @@

Source code for multiassayexperiment.MultiAssayExperiment

self._column_data = _sanitize_frame(column_data) elif sample_map is None and column_data is None: # make a sample map - self._column_data, self._sample_map = _create_smap_from_experiments( - self._experiments - ) + self._column_data, self._sample_map = _create_smap_from_experiments(self._experiments) else: raise ValueError( "Either 'sample_map' or 'column_data' is `None`. Either both should be provided or set both to `None`." @@ -567,7 +555,9 @@

Source code for multiassayexperiment.MultiAssayExperiment

for idx in range(len(self.experiment_names)): expt_name = self.experiment_names[idx] expt = self._experiments[expt_name] - output += f"[{idx}] {expt_name}: {type(expt).__name__} with {expt.shape[0]} rows and {expt.shape[1]} columns \n" # noqa + output += ( + f"[{idx}] {expt_name}: {type(expt).__name__} with {expt.shape[0]} rows and {expt.shape[1]} columns \n" # noqa + ) output += f"column_data columns({len(self._column_data.column_names)}): " output += f"{ut.print_truncated_list(self._column_data.column_names)}\n" @@ -598,9 +588,7 @@

Source code for multiassayexperiment.MultiAssayExperiment

[docs] - def set_experiments( - self, experiments: Dict[str, Any], in_place: bool = False - ) -> "MultiAssayExperiment": + def set_experiments(self, experiments: Dict[str, Any], in_place: bool = False) -> "MultiAssayExperiment": """Set new experiments. Args: @@ -672,9 +660,7 @@

Source code for multiassayexperiment.MultiAssayExperiment

[docs] - def set_experiment_names( - self, names: List[str], in_place: bool = False - ) -> "MultiAssayExperiment": + def set_experiment_names(self, names: List[str], in_place: bool = False) -> "MultiAssayExperiment": """Replace :py:attr:`~experiments`'s names. Args: @@ -690,9 +676,7 @@

Source code for multiassayexperiment.MultiAssayExperiment

""" current_names = self.get_experiment_names() if len(names) != len(current_names): - raise ValueError( - "Length of 'names' does not match the number of `experiments`." - ) + raise ValueError("Length of 'names' does not match the number of `experiments`.") new_experiments = OrderedDict() for idx in range(len(names)): @@ -766,9 +750,7 @@

Source code for multiassayexperiment.MultiAssayExperiment

expt = self.experiments[name] else: - raise TypeError( - f"'experiment' must be a string or integer, provided '{type(name)}'." - ) + raise TypeError(f"'experiment' must be a string or integer, provided '{type(name)}'.") if with_sample_data is True: assay_splits = self.sample_map.split("assay", only_indices=True) @@ -776,13 +758,9 @@

Source code for multiassayexperiment.MultiAssayExperiment

subset_map = subset_map.set_row_names(subset_map.get_column("colname")) expt_column_data = expt.column_data - new_column_data = biocframe.merge( - [subset_map, expt_column_data], join="outer" - ) + new_column_data = biocframe.merge([subset_map, expt_column_data], join="outer") - new_column_data = biocframe.merge( - [new_column_data, self._column_data], join="left" - ) + new_column_data = biocframe.merge([new_column_data, self._column_data], join="left") return expt.set_column_data(new_column_data, in_place=False) @@ -816,9 +794,7 @@

Source code for multiassayexperiment.MultiAssayExperiment

[docs] - def set_sample_map( - self, sample_map: biocframe.BiocFrame, in_place: bool = False - ) -> "MultiAssayExperiment": + def set_sample_map(self, sample_map: biocframe.BiocFrame, in_place: bool = False) -> "MultiAssayExperiment": """Set new sample mapping. Args: @@ -874,9 +850,7 @@

Source code for multiassayexperiment.MultiAssayExperiment

[docs] - def set_column_data( - self, column_data: biocframe.BiocFrame, in_place: bool = False - ) -> "MultiAssayExperiment": + def set_column_data(self, column_data: biocframe.BiocFrame, in_place: bool = False) -> "MultiAssayExperiment": """Set new sample metadata. Args: @@ -933,9 +907,7 @@

Source code for multiassayexperiment.MultiAssayExperiment

[docs] - def set_metadata( - self, metadata: dict, in_place: bool = False - ) -> "MultiAssayExperiment": + def set_metadata(self, metadata: dict, in_place: bool = False) -> "MultiAssayExperiment": """Set additional metadata. Args: @@ -950,9 +922,7 @@

Source code for multiassayexperiment.MultiAssayExperiment

or as a reference to the (in-place-modified) original. """ if not isinstance(metadata, dict): - raise TypeError( - f"`metadata` must be a dictionary, provided {type(metadata)}." - ) + raise TypeError(f"`metadata` must be a dictionary, provided {type(metadata)}.") output = self._define_output(in_place) output._metadata = metadata return output
@@ -982,9 +952,7 @@

Source code for multiassayexperiment.MultiAssayExperiment

def _normalize_column_slice(self, columns: Union[str, int, bool, Sequence, slice]): _scalar = None if columns != slice(None): - columns, _scalar = ut.normalize_subscript( - columns, len(self._column_data), self._column_data.row_names - ) + columns, _scalar = ut.normalize_subscript(columns, len(self._column_data), self._column_data.row_names) return columns, _scalar @@ -1044,9 +1012,7 @@

Source code for multiassayexperiment.MultiAssayExperiment

experiment_names = slice(None) if experiment_names != slice(None): - expts, _ = ut.normalize_subscript( - experiment_names, len(self.experiment_names), self.experiment_names - ) + expts, _ = ut.normalize_subscript(experiment_names, len(self.experiment_names), self.experiment_names) to_keep = [self.experiment_names[idx] for idx in expts] @@ -1125,9 +1091,7 @@

Source code for multiassayexperiment.MultiAssayExperiment

if experiments is None: experiments = slice(None) - _new_experiments = self.subset_experiments( - experiment_names=experiments, rows=rows, columns=columns - ) + _new_experiments = self.subset_experiments(experiment_names=experiments, rows=rows, columns=columns) # filter sample_map smap_indices_to_keep = [] @@ -1147,9 +1111,7 @@

Source code for multiassayexperiment.MultiAssayExperiment

[docs] - def subset_by_experiments( - self, experiments: Union[str, int, bool, Sequence] - ) -> "MultiAssayExperiment": + def subset_by_experiments(self, experiments: Union[str, int, bool, Sequence]) -> "MultiAssayExperiment": """Subset by experiment(s). Args: @@ -1166,16 +1128,12 @@

Source code for multiassayexperiment.MultiAssayExperiment

A new `MultiAssayExperiment` with the subset experiments. """ sresult = self._generic_slice(experiments=experiments) - return MultiAssayExperiment( - sresult.experiments, sresult.column_data, sresult.sample_map, self.metadata - )
+ return MultiAssayExperiment(sresult.experiments, sresult.column_data, sresult.sample_map, self.metadata)
[docs] - def subset_by_row( - self, rows: Union[str, int, bool, Sequence] - ) -> "MultiAssayExperiment": + def subset_by_row(self, rows: Union[str, int, bool, Sequence]) -> "MultiAssayExperiment": """Subset by rows. Args: @@ -1190,16 +1148,12 @@

Source code for multiassayexperiment.MultiAssayExperiment

A new `MultiAssayExperiment` with the subsetted rows. """ sresult = self._generic_slice(rows=rows) - return MultiAssayExperiment( - sresult.experiments, sresult.column_data, sresult.sample_map, self.metadata - )
+ return MultiAssayExperiment(sresult.experiments, sresult.column_data, sresult.sample_map, self.metadata)
[docs] - def subset_by_column( - self, columns: Union[str, int, bool, Sequence] - ) -> "MultiAssayExperiment": + def subset_by_column(self, columns: Union[str, int, bool, Sequence]) -> "MultiAssayExperiment": """Subset by column. Args: @@ -1214,9 +1168,7 @@

Source code for multiassayexperiment.MultiAssayExperiment

A new `MultiAssayExperiment` with the subsetted columns. """ sresult = self._generic_slice(columns=columns) - return MultiAssayExperiment( - sresult.experiments, sresult.column_data, sresult.sample_map, self.metadata - )
+ return MultiAssayExperiment(sresult.experiments, sresult.column_data, sresult.sample_map, self.metadata)
@@ -1260,9 +1212,7 @@

Source code for multiassayexperiment.MultiAssayExperiment

self.metadata, ) elif len(args) == 3: - sresult = self._generic_slice( - rows=args[0], columns=args[1], experiments=args[2] - ) + sresult = self._generic_slice(rows=args[0], columns=args[1], experiments=args[2]) return MultiAssayExperiment( sresult.experiments, sresult.column_data, @@ -1589,9 +1539,7 @@

Source code for multiassayexperiment.MultiAssayExperiment

samples.append(asy_sample) - sample_map = biocframe.BiocFrame( - {"assay": _all_assays, "primary": _all_primary, "colname": _all_colnames} - ) + sample_map = biocframe.BiocFrame({"assay": _all_assays, "primary": _all_primary, "colname": _all_colnames}) col_data = biocframe.BiocFrame({"samples": samples}, row_names=samples) return cls( @@ -1605,9 +1553,7 @@

Source code for multiassayexperiment.MultiAssayExperiment

[docs] @classmethod - def from_anndata( - cls, input: "anndata.AnnData", name: str = "unknown" - ) -> "MultiAssayExperiment": + def from_anndata(cls, input: "anndata.AnnData", name: str = "unknown") -> "MultiAssayExperiment": """Create a ``MultiAssayExperiment`` from :py:class:`~anndata.AnnData`. Since :py:class:`~anndata.AnnData` does not contain sample information, @@ -1634,9 +1580,7 @@

Source code for multiassayexperiment.MultiAssayExperiment

experiments = {name: scexpt} - col_data = biocframe.BiocFrame( - {"samples": ["unknown_sample"]}, row_names=["unknown_sample"] - ) + col_data = biocframe.BiocFrame({"samples": ["unknown_sample"]}, row_names=["unknown_sample"]) colnames = None @@ -1703,8 +1647,8 @@

Source code for multiassayexperiment.MultiAssayExperiment

- +
+ diff --git a/_modules/multiassayexperiment/io/h5ad.html b/_modules/multiassayexperiment/io/h5ad.html index 573b731..91d49cc 100644 --- a/_modules/multiassayexperiment/io/h5ad.html +++ b/_modules/multiassayexperiment/io/h5ad.html @@ -4,8 +4,8 @@ - - multiassayexperiment.io.h5ad - MultiAssayExperiment 0.4.4 documentation + + multiassayexperiment.io.h5ad - MultiAssayExperiment 0.5.0 documentation @@ -166,7 +166,7 @@
-
MultiAssayExperiment 0.4.4 documentation
 +
MultiAssayExperiment 0.5.0 documentation
@@ -190,7 +190,7 @@
- MultiAssayExperiment 0.4.4 documentation + MultiAssayExperiment 0.5.0 documentation @@ -305,8 +305,8 @@

Source code for multiassayexperiment.io.h5ad
-
- +
+ diff --git a/_modules/multiassayexperiment/io/interface.html b/_modules/multiassayexperiment/io/interface.html index e3142af..ba8c56e 100644 --- a/_modules/multiassayexperiment/io/interface.html +++ b/_modules/multiassayexperiment/io/interface.html @@ -4,8 +4,8 @@ - - multiassayexperiment.io.interface - MultiAssayExperiment 0.4.4 documentation + + multiassayexperiment.io.interface - MultiAssayExperiment 0.5.0 documentation @@ -166,7 +166,7 @@
-
MultiAssayExperiment 0.4.4 documentation
 +
MultiAssayExperiment 0.5.0 documentation
@@ -190,7 +190,7 @@
- MultiAssayExperiment 0.4.4 documentation + MultiAssayExperiment 0.5.0 documentation @@ -296,9 +296,7 @@

Source code for multiassayexperiment.io.interface

failedExpts = [] for expname, expt in experiments.items(): - if not ( - isinstance(expt, AnnData) or issubclass(type(expt), SummarizedExperiment) - ): + if not (isinstance(expt, AnnData) or issubclass(type(expt), SummarizedExperiment)): failedExpts.append(expname) if len(failedExpts) > 0: @@ -354,8 +352,8 @@

Source code for multiassayexperiment.io.interface

-
- +
+ diff --git a/_sources/changelog.md.txt b/_sources/changelog.md.txt index 00513bb..e61a338 100644 --- a/_sources/changelog.md.txt +++ b/_sources/changelog.md.txt @@ -1,5 +1,10 @@ # Changelog +## Version 0.5.0 + +- chore: Remove Python 3.8 (EOL) +- precommit: Replace docformatter with ruff's formatter + ## Version 0.4.1 - 0.4.3 - Access an experiment by index. diff --git a/_static/basic.css b/_static/basic.css index f316efc..7ebbd6d 100644 --- a/_static/basic.css +++ b/_static/basic.css @@ -1,12 +1,5 @@ /* - * basic.css - * ~~~~~~~~~ - * * Sphinx stylesheet -- basic theme. - * - * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * */ /* -- main layout ----------------------------------------------------------- */ @@ -115,15 +108,11 @@ img { /* -- search page ----------------------------------------------------------- */ ul.search { - margin: 10px 0 0 20px; - padding: 0; + margin-top: 10px; } ul.search li { - padding: 5px 0 5px 20px; - background-image: url(file.png); - background-repeat: no-repeat; - background-position: 0 7px; + padding: 5px 0; } ul.search li a { diff --git a/_static/doctools.js b/_static/doctools.js index 4d67807..0398ebb 100644 --- a/_static/doctools.js +++ b/_static/doctools.js @@ -1,12 +1,5 @@ /* - * doctools.js - * ~~~~~~~~~~~ - * * Base JavaScript utilities for all Sphinx HTML documentation. - * - * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * */ "use strict"; diff --git a/_static/documentation_options.js b/_static/documentation_options.js index f2671f2..240446d 100644 --- a/_static/documentation_options.js +++ b/_static/documentation_options.js @@ -1,5 +1,5 @@ const DOCUMENTATION_OPTIONS = { - VERSION: '0.4.4', + VERSION: '0.5.0', LANGUAGE: 'en', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/_static/language_data.js b/_static/language_data.js index 367b8ed..c7fe6c6 100644 --- a/_static/language_data.js +++ b/_static/language_data.js @@ -1,13 +1,6 @@ /* - * language_data.js - * ~~~~~~~~~~~~~~~~ - * * This script contains the language-specific data used by searchtools.js, * namely the list of stopwords, stemmer, scorer and splitter. - * - * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * */ var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; diff --git a/_static/searchtools.js b/_static/searchtools.js index b08d58c..2c774d1 100644 --- a/_static/searchtools.js +++ b/_static/searchtools.js @@ -1,12 +1,5 @@ /* - * searchtools.js - * ~~~~~~~~~~~~~~~~ - * * Sphinx JavaScript utilities for the full-text search. - * - * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * */ "use strict"; @@ -20,7 +13,7 @@ if (typeof Scorer === "undefined") { // and returns the new score. /* score: result => { - const [docname, title, anchor, descr, score, filename] = result + const [docname, title, anchor, descr, score, filename, kind] = result return score }, */ @@ -47,6 +40,14 @@ if (typeof Scorer === "undefined") { }; } +// Global search result kind enum, used by themes to style search results. +class SearchResultKind { + static get index() { return "index"; } + static get object() { return "object"; } + static get text() { return "text"; } + static get title() { return "title"; } +} + const _removeChildren = (element) => { while (element && element.lastChild) element.removeChild(element.lastChild); }; @@ -64,9 +65,13 @@ const _displayItem = (item, searchTerms, highlightTerms) => { const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; const contentRoot = document.documentElement.dataset.content_root; - const [docName, title, anchor, descr, score, _filename] = item; + const [docName, title, anchor, descr, score, _filename, kind] = item; let listItem = document.createElement("li"); + // Add a class representing the item's type: + // can be used by a theme's CSS selector for styling + // See SearchResultKind for the class names. + listItem.classList.add(`kind-${kind}`); let requestUrl; let linkUrl; if (docBuilder === "dirhtml") { @@ -115,8 +120,10 @@ const _finishSearch = (resultCount) => { "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." ); else - Search.status.innerText = _( - "Search finished, found ${resultCount} page(s) matching the search query." + Search.status.innerText = Documentation.ngettext( + "Search finished, found one page matching the search query.", + "Search finished, found ${resultCount} pages matching the search query.", + resultCount, ).replace('${resultCount}', resultCount); }; const _displayNextItem = ( @@ -138,7 +145,7 @@ const _displayNextItem = ( else _finishSearch(resultCount); }; // Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename]. +// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. // Order the results by score (in opposite order of appearance, since the // `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. const _orderResultsByScoreThenName = (a, b) => { @@ -248,6 +255,7 @@ const Search = { searchSummary.classList.add("search-summary"); searchSummary.innerText = ""; const searchList = document.createElement("ul"); + searchList.setAttribute("role", "list"); searchList.classList.add("search"); const out = document.getElementById("search-results"); @@ -318,7 +326,7 @@ const Search = { const indexEntries = Search._index.indexentries; // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename]. + // Each is an array of [docname, title, anchor, descr, score, filename, kind]. const normalResults = []; const nonMainIndexResults = []; @@ -337,6 +345,7 @@ const Search = { null, score + boost, filenames[file], + SearchResultKind.title, ]); } } @@ -354,6 +363,7 @@ const Search = { null, score, filenames[file], + SearchResultKind.index, ]; if (isMain) { normalResults.push(result); @@ -475,6 +485,7 @@ const Search = { descr, score, filenames[match[0]], + SearchResultKind.object, ]); }; Object.keys(objects).forEach((prefix) => @@ -585,6 +596,7 @@ const Search = { null, score, filenames[file], + SearchResultKind.text, ]); } return results; diff --git a/api/modules.html b/api/modules.html index 7a9fb92..6e4af9b 100644 --- a/api/modules.html +++ b/api/modules.html @@ -5,8 +5,8 @@ - - multiassayexperiment - MultiAssayExperiment 0.4.4 documentation + + multiassayexperiment - MultiAssayExperiment 0.5.0 documentation @@ -167,7 +167,7 @@
-
MultiAssayExperiment 0.4.4 documentation
 +
MultiAssayExperiment 0.5.0 documentation
@@ -191,7 +191,7 @@
- MultiAssayExperiment 0.4.4 documentation + MultiAssayExperiment 0.5.0 documentation @@ -315,6 +315,7 @@

multiassayexperiment
  • SlicerResult
    • SlicerResult.__getnewargs__()
      • +
    • SlicerResult.__match_args__
    • SlicerResult.__new__()
    • SlicerResult.__repr__()
    • SlicerResult.__slots__
      • @@ -381,8 +382,8 @@

      multiassayexperiment

    • -
    - +
    + diff --git a/api/multiassayexperiment.html b/api/multiassayexperiment.html index 8de2106..a666f3e 100644 --- a/api/multiassayexperiment.html +++ b/api/multiassayexperiment.html @@ -5,8 +5,8 @@ - - multiassayexperiment package - MultiAssayExperiment 0.4.4 documentation + + multiassayexperiment package - MultiAssayExperiment 0.5.0 documentation @@ -167,7 +167,7 @@
    -
    MultiAssayExperiment 0.4.4 documentation
     +
    MultiAssayExperiment 0.5.0 documentation
    @@ -191,7 +191,7 @@
    - MultiAssayExperiment 0.4.4 documentation + MultiAssayExperiment 0.5.0 documentation @@ -282,7 +282,7 @@

    Submodules
    class multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment(experiments, column_data=None, sample_map=None, metadata=None, validate=True)[source]¶
    -

    Bases: object

    +

    Bases: object

    Container class for representing and managing multi-omics genomic experiments.

    Checkout the R/MultiAssayExperiment @@ -313,13 +313,13 @@

    Submodules
    Parameters:
    -

    args (tuple) –

    Tuple containing slices along dimensions (rows, columns, experiments).

    +

    args (tuple) –

    Tuple containing slices along dimensions (rows, columns, experiments).

    Each element in the tuple, might be either a integer vector (integer positions), -boolean vector or slice object. Defaults to None.

    +boolean vector or slice object. Defaults to None.

    Raises:
    -

    ValueError – Too many or too few slices.

    +

    ValueError – Too many or too few slices.

    Return type:

    MultiAssayExperiment

    @@ -335,7 +335,7 @@

    Submodules__repr__()[source]¶
    Return type:
    -

    str

    +

    str

    Returns:

    A string representation.

    @@ -355,13 +355,13 @@

    Submodules
    Parameters:
      -

    • name (str) – Name of the new experiment.

      • -

    • experiment (Any) – The experiment to add.

      • -

    • sample_map (BiocFrame) – Sample map to append to the MAE.

      • -

    • column_data (Optional[BiocFrame]) –

      Sample data to append to the MAE.

      +

    • name (str) – Name of the new experiment.

      • +

    • experiment (Any) – The experiment to add.

      • +

    • sample_map (BiocFrame) – Sample map to append to the MAE.

      • +

    • column_data (Optional[BiocFrame]) –

      Sample data to append to the MAE.

      Defaults to None.

      • -

    • in_place (bool) – Whether to modify the MultiAssayExperiment in place. +

    • in_place (bool) – Whether to modify the MultiAssayExperiment in place. Defaults to False.

    @@ -377,31 +377,31 @@

    Submodules
    -property assays: Dict[str, Any]¶
    +property assays: Dict[str, Any]¶

    Alias for get_experiments().

    -property colnames: Dict[str, Names | None]¶
    +property colnames: Dict[str, Names | None]¶

    Alias for get_column_names, provided for back-compatibility.

    -property column_data: BiocFrame¶
    +property column_data: BiocFrame¶

    Alias for get_column_data().

    -property column_names: Dict[str, Names | None]¶
    +property column_names: Dict[str, Names | None]¶

    Alias for get_column_names, provided for back-compatibility.

    -property columnnames: Dict[str, Names | None]¶
    +property columnnames: Dict[str, Names | None]¶

    Alias for get_column_names, provided for back-compatibility.

    @@ -411,7 +411,7 @@

    Submodules
    Return type:
    -

    Sequence[bool]

    +

    Sequence[bool]

    Returns:

    A boolean vector same as the number of samples in ‘column_data’, @@ -433,8 +433,8 @@

    Submodules
    Parameters:
      -

    • name (Union[int, str]) – Name or index position of the experiment.

      • -

    • with_sample_data (bool) –

      Whether to merge column data of the experiment with +

    • name (Union[int, str]) – Name or index position of the experiment.

      • +

    • with_sample_data (bool) –

      Whether to merge column data of the experiment with sample_data from the MAE.

      Defaults to False.

      • @@ -442,12 +442,12 @@

      SubmodulesRaises:
        -

      • AttributeError – If the experiment name does not exist.

        • -

      • IndexError – If index is greater than the number of experiments.

        • +

      • AttributeError – If the experiment name does not exist.

        • +

      • IndexError – If index is greater than the number of experiments.

      Return type:
      -

      Any

      +

      Any

      Returns:

      The experiment object.

      @@ -459,13 +459,13 @@

      Submodules
      -property experiment_names: List[str]¶
      +property experiment_names: List[str]¶

      Alias for get_experiment_names().

      -property experiments: Dict[str, Any]¶
      +property experiments: Dict[str, Any]¶

      Alias for get_experiments().

      @@ -475,7 +475,7 @@

      Submodules
      Return type:
      -

      List[str]

      +

      List[str]

      @@ -483,8 +483,8 @@

      Submodules
      classmethod from_anndata(input, name='unknown')[source]¶
      -

      Create a MultiAssayExperiment from AnnData.

      -

      Since AnnData does not contain sample information, +

      Create a MultiAssayExperiment from AnnData.

      +

      Since AnnData does not contain sample information, sample named "unknown_sample" will be added to col_data. All cells are considered to be extracted from this sample and is reflected in @@ -493,7 +493,7 @@

      SubmodulesParameters:

      • input (anndata.AnnData) – An AnnData object.

        • -

      • name (str) –

        Name for the experiment.

        +

      • name (str) –

        Name for the experiment.

        Defaults to “unknown”.

      @@ -520,7 +520,7 @@

      Submodules

      input (mudata.MuData) – MuData object.

      Raises:
      -

      Exception – If mudata object is read in backed mode isbacked.

      +

      Exception – If mudata object is read in backed mode isbacked.

      Return type:

      MultiAssayExperiment

      @@ -537,10 +537,10 @@

      Submodules
      Return type:
      -

      BiocFrame

      +

      BiocFrame

      Returns:
      -

      A BiocFrame containing sample metadata.

      +

      A BiocFrame containing sample metadata.

      @@ -550,7 +550,7 @@

      Submodulesget_column_names()[source]¶
      Return type:
      -

      Dict[str, Optional[Names]]

      +

      Dict[str, Optional[Names]]

      Returns:

      Dictionary, with experiment names as keys, and the column names as values.

      @@ -564,7 +564,7 @@

      Submodules
      Return type:
      -

      List[str]

      +

      List[str]

      Returns:

      List of experiment names.

      @@ -578,7 +578,7 @@

      Submodules
      Return type:
      -

      Dict[str, Any]

      +

      Dict[str, Any]

      Returns:

      A dictionary of all experiments, with experiment @@ -592,7 +592,7 @@

      Submodulesget_metadata()[source]¶
      Return type:
      -

      dict

      +

      dict

      Returns:

      Dictionary of metadata for this object.

      @@ -605,7 +605,7 @@

      Submodulesget_row_names()[source]¶
      Return type:
      -

      Dict[str, Optional[Names]]

      +

      Dict[str, Optional[Names]]

      Returns:

      Dictionary, with experiment names as keys, and row names as values.

      @@ -619,10 +619,10 @@

      Submodules
      Return type:
      -

      BiocFrame

      +

      BiocFrame

      Returns:
      -

      A BiocFrame with sample mapping information.

      +

      A BiocFrame with sample mapping information.

      @@ -634,7 +634,7 @@

      Submodules
      Return type:
      -

      Any

      +

      Any

      @@ -655,7 +655,7 @@

      Submodules
      -property metadata: dict¶
      +property metadata: dict¶

      Alias for get_metadata.

      @@ -665,7 +665,7 @@

      Submodules
      Return type:
      -

      Dict[str, Dict[str, Sequence[bool]]]

      +

      Dict[str, Dict[str, Sequence[bool]]]

      Returns:

      A dictionary where experiment names @@ -676,13 +676,13 @@

      Submodules
      -property rownames: Dict[str, Names | None]¶
      +property rownames: Dict[str, Names | None]¶

      Alias for get_row_names, provided for back-compatibility.

      -property sample_map: BiocFrame¶
      +property sample_map: BiocFrame¶

      Alias for get_sample_map().

      @@ -693,8 +693,8 @@

      Submodules
      Parameters:
        -

      • column_data (BiocFrame) – New sample metadata.

        • -

      • in_place (bool) – Whether to modify the MultiAssayExperiment in place.

        • +

      • column_data (BiocFrame) – New sample metadata.

        • +

      • in_place (bool) – Whether to modify the MultiAssayExperiment in place.

      Return type:
      @@ -714,8 +714,8 @@

      Submodules
      Parameters:
        -

      • names (List[str]) – New names.

        • -

      • in_place (bool) – Whether to modify the MultiAssayExperiment in place.

        • +

      • names (List[str]) – New names.

        • +

      • in_place (bool) – Whether to modify the MultiAssayExperiment in place.

      Return type:
      @@ -735,13 +735,13 @@

      Submodules
      Parameters:
        -

      • experiments (Dict[str, Any]) –

        New experiments to set. A dictionary of experiments with experiment names as keys and +

      • experiments (Dict[str, Any]) –

        New experiments to set. A dictionary of experiments with experiment names as keys and the experiments as values.

        Each experiment may be either a -SummarizedExperiment +SummarizedExperiment or any class that extends SummarizedExperiment.

        • -

      • in_place (bool) – Whether to modify the MultiAssayExperiment in place.

        • +

      • in_place (bool) – Whether to modify the MultiAssayExperiment in place.

      Return type:
      @@ -761,8 +761,8 @@

      Submodules
      Parameters:
        -

      • metadata (dict) – New metadata for this object.

        • -

      • in_place (bool) – Whether to modify the MultiAssayExperiment in place.

        • +

      • metadata (dict) – New metadata for this object.

        • +

      • in_place (bool) – Whether to modify the MultiAssayExperiment in place.

      Return type:
      @@ -782,8 +782,8 @@

      Submodules
      Parameters:
        -

      • sample_map (BiocFrame) – New sample map.

        • -

      • in_place (bool) – Whether to modify the MultiAssayExperiment in place.

        • +

      • sample_map (BiocFrame) – New sample map.

        • +

      • in_place (bool) – Whether to modify the MultiAssayExperiment in place.

      Return type:
      @@ -802,7 +802,7 @@

      Submodules
      Parameters:
      -

      columns (Union[str, int, bool, Sequence]) –

      Columns to be extracted.

      +

      columns (Union[str, int, bool, Sequence]) –

      Columns to be extracted.

      Integer indices, a boolean filter, or (if the current object is named) names specifying the ranges to be extracted, see normalize_subscript().

      @@ -823,7 +823,7 @@

      Submodules
      Parameters:
      -

      experiments (Union[str, int, bool, Sequence]) –

      Experiments to extract.

      +

      experiments (Union[str, int, bool, Sequence]) –

      Experiments to extract.

      Integer indices, a boolean filter, or (if the current object is named) names specifying the ranges to be extracted, see normalize_subscript().

      @@ -845,7 +845,7 @@

      Submodules
      Parameters:
      -

      rows (Union[str, int, bool, Sequence]) –

      Rows to be extracted.

      +

      rows (Union[str, int, bool, Sequence]) –

      Rows to be extracted.

      Integer indices, a boolean filter, or (if the current object is named) names specifying the ranges to be extracted, see normalize_subscript().

      @@ -867,17 +867,17 @@

      Submodules
      Parameters:
        -

      • rows (Union[str, int, bool, Sequence, None]) –

        Row indices to subset.

        +

      • rows (Union[str, int, bool, Sequence, None]) –

        Row indices to subset.

        Integer indices, a boolean filter, or (if the current object is named) names specifying the ranges to be extracted, see normalize_subscript().

        • -

      • columns (Union[str, int, bool, Sequence, None]) –

        Column indices (from column_data) to subset.

        +

      • columns (Union[str, int, bool, Sequence, None]) –

        Column indices (from column_data) to subset.

        Integer indices, a boolean filter, or (if the current object is named) names specifying the ranges to be extracted, see normalize_subscript().

        • -

      • experiment_names (Union[str, int, bool, Sequence]) –

        Experiment names to keep.

        +

      • experiment_names (Union[str, int, bool, Sequence]) –

        Experiment names to keep.

        Integer indices, a boolean filter, or (if the current object is named) names specifying the ranges to be extracted, see normalize_subscript().

        @@ -886,7 +886,7 @@

        SubmodulesReturn type: -

        Dict[str, Any]

        +

        Dict[str, Any]

        Returns:

        A dictionary with experiment names as keys @@ -911,13 +911,18 @@

        Submodules
        class multiassayexperiment.MultiAssayExperiment.SlicerResult(experiments, sample_map, column_data)¶
        -

        Bases: tuple

        +

        Bases: tuple

        __getnewargs__()¶

        Return self as a plain tuple. Used by copy and pickle.

        +
        +
        +__match_args__ = ('experiments', 'sample_map', 'column_data')¶
        +
        +
        static __new__(_cls, experiments, sample_map, column_data)¶
        @@ -1066,6 +1071,7 @@

        SubmodulesSlicerResult
        • SlicerResult.__getnewargs__()
          • +
        • SlicerResult.__match_args__
        • SlicerResult.__new__()
        • SlicerResult.__repr__()
        • SlicerResult.__slots__
          • @@ -1088,8 +1094,8 @@

          Submodules - +

    + diff --git a/api/multiassayexperiment.io.html b/api/multiassayexperiment.io.html index 410276c..fb6faae 100644 --- a/api/multiassayexperiment.io.html +++ b/api/multiassayexperiment.io.html @@ -5,8 +5,8 @@ - - multiassayexperiment.io package - MultiAssayExperiment 0.4.4 documentation + + multiassayexperiment.io package - MultiAssayExperiment 0.5.0 documentation @@ -167,7 +167,7 @@
    -
    MultiAssayExperiment 0.4.4 documentation
     +
    MultiAssayExperiment 0.5.0 documentation
    @@ -191,7 +191,7 @@
    - MultiAssayExperiment 0.4.4 documentation + MultiAssayExperiment 0.5.0 documentation @@ -267,7 +267,7 @@

    Submodulesfrom_anndata().

    Parameters:
    -

    path (str) – Path to a H5AD file

    +

    path (str) – Path to a H5AD file

    Return type:

    MultiAssayExperiment

    @@ -285,9 +285,9 @@

    Submodules multiassayexperiment.io.interface.make_mae(experiments)[source]¶

    Create an MultiAssayExperiment from a dictionary of -experiment objects. Each experiment is either an AnnData object or a subclass of -SummarizedExperiment. AnnData objects -will be converted to a SingleCellExperiment.

    +experiment objects. Each experiment is either an AnnData object or a subclass of +SummarizedExperiment. AnnData objects +will be converted to a SingleCellExperiment.

    The import naively creates sample mapping, with each experiment considered to be a independent sample. We add a sample to col_data @@ -296,14 +296,14 @@

    Submodulessample_map.

    Parameters:
    -

    experiments (Dict[str, Any]) –

    A dictionary of experiments with experiment names as keys and the +

    experiments (Dict[str, Any]) –

    A dictionary of experiments with experiment names as keys and the experiments as values.

    -

    Each experiment can be either a AnnData object or a -subclass of SummarizedExperiment.

    +

    Each experiment can be either a AnnData object or a +subclass of SummarizedExperiment.

    Raises:
    -

    TypeError –

      +

      TypeError –

      • If any of the provided objects are not an expected types. - If experiments is not a dictionary.

      @@ -401,8 +401,8 @@

      Submodules - +

    + diff --git a/authors.html b/authors.html index 4d61d10..08f7333 100644 --- a/authors.html +++ b/authors.html @@ -5,8 +5,8 @@ - - Contributors - MultiAssayExperiment 0.4.4 documentation + + Contributors - MultiAssayExperiment 0.5.0 documentation @@ -167,7 +167,7 @@
    -
    MultiAssayExperiment 0.4.4 documentation
     +
    MultiAssayExperiment 0.5.0 documentation
    @@ -191,7 +191,7 @@
    - MultiAssayExperiment 0.4.4 documentation + MultiAssayExperiment 0.5.0 documentation @@ -308,8 +308,8 @@

    Contributors - +

    + diff --git a/changelog.html b/changelog.html index fbf313a..68b3e11 100644 --- a/changelog.html +++ b/changelog.html @@ -5,8 +5,8 @@ - - Changelog - MultiAssayExperiment 0.4.4 documentation + + Changelog - MultiAssayExperiment 0.5.0 documentation @@ -167,7 +167,7 @@
    -
    MultiAssayExperiment 0.4.4 documentation
     +
    MultiAssayExperiment 0.5.0 documentation
    @@ -191,7 +191,7 @@
    - MultiAssayExperiment 0.4.4 documentation + MultiAssayExperiment 0.5.0 documentation @@ -254,6 +254,13 @@

    Changelog¶

    +
    +

    Version 0.5.0¶

    +
      +

    • chore: Remove Python 3.8 (EOL)

      • +

    • precommit: Replace docformatter with ruff’s formatter

      • +
    +

    Version 0.4.1 - 0.4.3¶

      @@ -353,6 +360,7 @@

      Version 0.1
      • Changelog
          +
        • Version 0.5.0
        • Version 0.4.1 - 0.4.3
        • Version 0.4.0
        • Version 0.3.0
          • @@ -369,8 +377,8 @@

          Version 0.1 - +

    + diff --git a/contributing.html b/contributing.html index 0ae33c5..eb21c78 100644 --- a/contributing.html +++ b/contributing.html @@ -5,8 +5,8 @@ - - Contributing - MultiAssayExperiment 0.4.4 documentation + + Contributing - MultiAssayExperiment 0.5.0 documentation @@ -167,7 +167,7 @@
    -
    MultiAssayExperiment 0.4.4 documentation
     +
    MultiAssayExperiment 0.5.0 documentation
    @@ -191,7 +191,7 @@
    - MultiAssayExperiment 0.4.4 documentation + MultiAssayExperiment 0.5.0 documentation @@ -477,6 +477,9 @@

    Releases

  • Run tox -e publish -- --repository pypi and check that everything was uploaded to PyPI correctly.

    • + + +
    @@ -487,9 +490,6 @@

    Releases of environments, including private companies and proprietary code bases.

    - - -

    @@ -573,8 +573,8 @@

    Releases

    -
    - +
    + diff --git a/genindex.html b/genindex.html index 7ddf9ef..ee391e5 100644 --- a/genindex.html +++ b/genindex.html @@ -4,7 +4,7 @@ - Index - MultiAssayExperiment 0.4.4 documentation + Index - MultiAssayExperiment 0.5.0 documentation @@ -165,7 +165,7 @@
    -
    MultiAssayExperiment 0.4.4 documentation
     +
    MultiAssayExperiment 0.5.0 documentation
    @@ -189,7 +189,7 @@
    - MultiAssayExperiment 0.4.4 documentation + MultiAssayExperiment 0.5.0 documentation @@ -263,6 +263,8 @@

    _

      +
    • __match_args__ (multiassayexperiment.MultiAssayExperiment.SlicerResult attribute) +
    • __new__() (multiassayexperiment.MultiAssayExperiment.SlicerResult static method)
    • __repr__() (multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment method) @@ -549,8 +551,8 @@

      T

    -
    - +
    + diff --git a/index.html b/index.html index adb22c4..a331b25 100644 --- a/index.html +++ b/index.html @@ -5,8 +5,8 @@ - - MultiAssayExperiment 0.4.4 documentation + + MultiAssayExperiment 0.5.0 documentation @@ -167,7 +167,7 @@
    -
    MultiAssayExperiment 0.4.4 documentation
     +
    MultiAssayExperiment 0.5.0 documentation
    @@ -191,7 +191,7 @@
    - MultiAssayExperiment 0.4.4 documentation + MultiAssayExperiment 0.5.0 documentation @@ -287,6 +287,7 @@

    Contents
  • License
  • Authors
  • Changelog
      +
    • Version 0.5.0
    • Version 0.4.1 - 0.4.3
    • Version 0.4.0
    • Version 0.3.0
      • @@ -367,8 +368,8 @@

      Indices and tables - +

    • + diff --git a/license.html b/license.html index fa088d4..9dfc1d1 100644 --- a/license.html +++ b/license.html @@ -5,8 +5,8 @@ - - License - MultiAssayExperiment 0.4.4 documentation + + License - MultiAssayExperiment 0.5.0 documentation @@ -167,7 +167,7 @@
    -
    MultiAssayExperiment 0.4.4 documentation
     +
    MultiAssayExperiment 0.5.0 documentation
    @@ -191,7 +191,7 @@
    - MultiAssayExperiment 0.4.4 documentation + MultiAssayExperiment 0.5.0 documentation @@ -328,8 +328,8 @@

    License¶

    -
    - +
    + diff --git a/objects.inv b/objects.inv index 0009fde..cffcf05 100644 Binary files a/objects.inv and b/objects.inv differ diff --git a/overview.html b/overview.html index 989f469..a6d2c47 100644 --- a/overview.html +++ b/overview.html @@ -5,8 +5,8 @@ - - Multiple experiments - MultiAssayExperiment 0.4.4 documentation + + Multiple experiments - MultiAssayExperiment 0.5.0 documentation @@ -167,7 +167,7 @@
    -
    MultiAssayExperiment 0.4.4 documentation
     +
    MultiAssayExperiment 0.5.0 documentation
    @@ -191,7 +191,7 @@
    - MultiAssayExperiment 0.4.4 documentation + MultiAssayExperiment 0.5.0 documentation @@ -462,6 +462,12 @@

    Interop with an spatial: 1000 x 50

    +
    /home/runner/work/MultiAssayExperiment/MultiAssayExperiment/.tox/docs/lib/python3.11/site-packages/mudata/_core/mudata.py:1531: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility.
+  self._update_attr("var", axis=0, join_common=join_common)
+/home/runner/work/MultiAssayExperiment/MultiAssayExperiment/.tox/docs/lib/python3.11/site-packages/mudata/_core/mudata.py:1429: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility.
+  self._update_attr("obs", axis=1, join_common=join_common)
+
    +

    Lets convert this object to an MAE:

    @@ -785,8 +791,8 @@

    Empty MAE - +

    + diff --git a/py-modindex.html b/py-modindex.html index 5cd8232..e0bbfe9 100644 --- a/py-modindex.html +++ b/py-modindex.html @@ -4,7 +4,7 @@ - Python Module Index - MultiAssayExperiment 0.4.4 documentation + Python Module Index - MultiAssayExperiment 0.5.0 documentation @@ -165,7 +165,7 @@
    -
    MultiAssayExperiment 0.4.4 documentation
     +
    MultiAssayExperiment 0.5.0 documentation
    @@ -189,7 +189,7 @@
    - MultiAssayExperiment 0.4.4 documentation + MultiAssayExperiment 0.5.0 documentation @@ -320,8 +320,8 @@

    Python Module Index

    -
    - +
    + diff --git a/readme.html b/readme.html index afd550a..9d6e327 100644 --- a/readme.html +++ b/readme.html @@ -5,8 +5,8 @@ - - MultiAssayExperiment - MultiAssayExperiment 0.4.4 documentation + + MultiAssayExperiment - MultiAssayExperiment 0.5.0 documentation @@ -167,7 +167,7 @@
    -
    MultiAssayExperiment 0.4.4 documentation
     +
    MultiAssayExperiment 0.5.0 documentation
    @@ -191,7 +191,7 @@
    - MultiAssayExperiment 0.4.4 documentation + MultiAssayExperiment 0.5.0 documentation @@ -423,8 +423,8 @@

    Note¶

    -
    - +
    + diff --git a/reports/overview.err.log b/reports/overview.err.log index d373412..e045f10 100644 --- a/reports/overview.err.log +++ b/reports/overview.err.log @@ -1,17 +1,20 @@ Traceback (most recent call last): - File "/home/runner/work/MultiAssayExperiment/MultiAssayExperiment/.tox/docs/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution + File "/home/runner/work/MultiAssayExperiment/MultiAssayExperiment/.tox/docs/lib/python3.11/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution executenb( - File "/home/runner/work/MultiAssayExperiment/MultiAssayExperiment/.tox/docs/lib/python3.9/site-packages/nbclient/client.py", line 1314, in execute + File "/home/runner/work/MultiAssayExperiment/MultiAssayExperiment/.tox/docs/lib/python3.11/site-packages/nbclient/client.py", line 1319, in execute return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() - File "/home/runner/work/MultiAssayExperiment/MultiAssayExperiment/.tox/docs/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/runner/work/MultiAssayExperiment/MultiAssayExperiment/.tox/docs/lib/python3.11/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped return loop.run_until_complete(inner) - File "/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/asyncio/base_events.py", line 654, in run_until_complete return future.result() - File "/home/runner/work/MultiAssayExperiment/MultiAssayExperiment/.tox/docs/lib/python3.9/site-packages/nbclient/client.py", line 709, in async_execute + ^^^^^^^^^^^^^^^ + File "/home/runner/work/MultiAssayExperiment/MultiAssayExperiment/.tox/docs/lib/python3.11/site-packages/nbclient/client.py", line 709, in async_execute await self.async_execute_cell( - File "/home/runner/work/MultiAssayExperiment/MultiAssayExperiment/.tox/docs/lib/python3.9/site-packages/nbclient/client.py", line 1062, in async_execute_cell + File "/home/runner/work/MultiAssayExperiment/MultiAssayExperiment/.tox/docs/lib/python3.11/site-packages/nbclient/client.py", line 1062, in async_execute_cell await self._check_raise_for_error(cell, cell_index, exec_reply) - File "/home/runner/work/MultiAssayExperiment/MultiAssayExperiment/.tox/docs/lib/python3.9/site-packages/nbclient/client.py", line 918, in _check_raise_for_error + File "/home/runner/work/MultiAssayExperiment/MultiAssayExperiment/.tox/docs/lib/python3.11/site-packages/nbclient/client.py", line 918, in _check_raise_for_error raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: ------------------ diff --git a/search.html b/search.html index 580b152..321d1cd 100644 --- a/search.html +++ b/search.html @@ -5,9 +5,9 @@ - + -Search - MultiAssayExperiment 0.4.4 documentation +Search - MultiAssayExperiment 0.5.0 documentation @@ -167,7 +167,7 @@
    -
    MultiAssayExperiment 0.4.4 documentation
     +
    MultiAssayExperiment 0.5.0 documentation
    @@ -191,7 +191,7 @@
    - MultiAssayExperiment 0.4.4 documentation + MultiAssayExperiment 0.5.0 documentation @@ -289,8 +289,8 @@
    -
    - +
    + diff --git a/searchindex.js b/searchindex.js index c86c01e..d5ee6aa 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"Access an experiment": [[8, "access-an-experiment"]], "Changelog": [[4, null]], "Clone the repository": [[5, "clone-the-repository"]], "Code Contributions": [[5, "code-contributions"]], "Complete cases": [[8, "complete-cases"]], "Construction": [[8, "construction"]], "Contents": [[6, "contents"]], "Contributing": [[5, "contributing"]], "Contributors": [[3, null]], "Create an environment": [[5, "create-an-environment"]], "Documentation Improvements": [[5, "documentation-improvements"]], "Empty MAE": [[8, "empty-mae"]], "Getters/Setters": [[8, "getters-setters"]], "Helper functions": [[8, "helper-functions"]], "Implement your changes": [[5, "implement-your-changes"]], "Indices and tables": [[6, "indices-and-tables"]], "Install": [[6, "install"], [9, "install"]], "Interop with anndata or mudata": [[8, "interop-with-anndata-or-mudata"]], "Intersect rows": [[8, "intersect-rows"]], "Issue Reports": [[5, "issue-reports"]], "License": [[7, null]], "Maintainer tasks": [[5, "maintainer-tasks"]], "Module contents": [[1, "module-multiassayexperiment"], [2, "module-multiassayexperiment.io"]], "MultiAssayExperiment": [[6, null], [9, null]], "Multiple experiments": [[8, null]], "No sample mapping?": [[8, "no-sample-mapping"]], "Note": [[9, "note"]], "Releases": [[5, "releases"]], "Replicates": [[8, "replicates"]], "Row or column name accessors": [[8, "row-or-column-name-accessors"]], "Setters": [[8, "setters"]], "Submit an issue": [[5, "submit-an-issue"]], "Submit your contribution": [[5, "submit-your-contribution"]], "Submodules": [[1, "submodules"], [2, "submodules"]], "Subpackages": [[1, "subpackages"]], "Subset by experiments dimension": [[8, "subset-by-experiments-dimension"]], "Subset by indices": [[8, "subset-by-indices"]], "Subsetting": [[8, "subsetting"]], "Todo": [[5, null], [5, "id2"], [5, "id3"], [5, "id5"], [5, "id6"], [5, "id7"], [5, "id8"], [5, "id9"], [5, "id10"], [5, "id11"], [5, "id12"]], "Troubleshooting": [[5, "troubleshooting"]], "Usage": [[9, "usage"]], "Version 0.1": [[4, "version-0-1"]], "Version 0.2.0": [[4, "version-0-2-0"]], "Version 0.3.0": [[4, "version-0-3-0"]], "Version 0.4.0": [[4, "version-0-4-0"]], "Version 0.4.1 - 0.4.3": [[4, "version-0-4-1-0-4-3"]], "multiassayexperiment": [[0, null]], "multiassayexperiment package": [[1, null]], "multiassayexperiment.MultiAssayExperiment module": [[1, "module-multiassayexperiment.MultiAssayExperiment"]], "multiassayexperiment.io package": [[2, null]], "multiassayexperiment.io.h5ad module": [[2, "module-multiassayexperiment.io.h5ad"]], "multiassayexperiment.io.interface module": [[2, "module-multiassayexperiment.io.interface"]]}, "docnames": ["api/modules", "api/multiassayexperiment", "api/multiassayexperiment.io", "authors", "changelog", "contributing", "index", "license", "overview", "readme"], "envversion": {"sphinx": 62, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1}, "filenames": ["api/modules.rst", "api/multiassayexperiment.rst", "api/multiassayexperiment.io.rst", "authors.md", "changelog.md", "contributing.md", "index.md", "license.md", "overview.md", "readme.md"], "indexentries": {"__copy__() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.__copy__", false]], "__deepcopy__() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.__deepcopy__", false]], "__getitem__() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.__getitem__", false]], "__getnewargs__() (multiassayexperiment.multiassayexperiment.slicerresult method)": [[1, "multiassayexperiment.MultiAssayExperiment.SlicerResult.__getnewargs__", false]], "__new__() (multiassayexperiment.multiassayexperiment.slicerresult static method)": [[1, "multiassayexperiment.MultiAssayExperiment.SlicerResult.__new__", false]], "__repr__() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.__repr__", false]], "__repr__() (multiassayexperiment.multiassayexperiment.slicerresult method)": [[1, "multiassayexperiment.MultiAssayExperiment.SlicerResult.__repr__", false]], "__slots__ (multiassayexperiment.multiassayexperiment.slicerresult attribute)": [[1, "multiassayexperiment.MultiAssayExperiment.SlicerResult.__slots__", false]], "add_experiment() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.add_experiment", false]], "assays (multiassayexperiment.multiassayexperiment.multiassayexperiment property)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.assays", false]], "colnames (multiassayexperiment.multiassayexperiment.multiassayexperiment property)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.colnames", false]], "column_data (multiassayexperiment.multiassayexperiment.multiassayexperiment property)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.column_data", false]], "column_data (multiassayexperiment.multiassayexperiment.slicerresult attribute)": [[1, "multiassayexperiment.MultiAssayExperiment.SlicerResult.column_data", false]], "column_names (multiassayexperiment.multiassayexperiment.multiassayexperiment property)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.column_names", false]], "columnnames (multiassayexperiment.multiassayexperiment.multiassayexperiment property)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.columnnames", false]], "complete_cases() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.complete_cases", false]], "copy() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.copy", false]], "experiment() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.experiment", false]], "experiment_names (multiassayexperiment.multiassayexperiment.multiassayexperiment property)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.experiment_names", false]], "experiments (multiassayexperiment.multiassayexperiment.multiassayexperiment property)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.experiments", false]], "experiments (multiassayexperiment.multiassayexperiment.slicerresult attribute)": [[1, "multiassayexperiment.MultiAssayExperiment.SlicerResult.experiments", false]], "find_common_row_names() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.find_common_row_names", false]], "from_anndata() (multiassayexperiment.multiassayexperiment.multiassayexperiment class method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.from_anndata", false]], "from_mudata() (multiassayexperiment.multiassayexperiment.multiassayexperiment class method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.from_mudata", false]], "get_column_data() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.get_column_data", false]], "get_column_names() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.get_column_names", false]], "get_experiment_names() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.get_experiment_names", false]], "get_experiments() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.get_experiments", false]], "get_metadata() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.get_metadata", false]], "get_row_names() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.get_row_names", false]], "get_sample_map() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.get_sample_map", false]], "get_with_column_data() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.get_with_column_data", false]], "intersect_rows() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.intersect_rows", false]], "make_mae() (in module multiassayexperiment.io.interface)": [[2, "multiassayexperiment.io.interface.make_mae", false]], "metadata (multiassayexperiment.multiassayexperiment.multiassayexperiment property)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.metadata", false]], "module": [[1, "module-multiassayexperiment", false], [1, "module-multiassayexperiment.MultiAssayExperiment", false], [2, "module-multiassayexperiment.io", false], [2, "module-multiassayexperiment.io.h5ad", false], [2, "module-multiassayexperiment.io.interface", false]], "multiassayexperiment": [[1, "module-multiassayexperiment", false]], "multiassayexperiment (class in multiassayexperiment.multiassayexperiment)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment", false]], "multiassayexperiment.io": [[2, "module-multiassayexperiment.io", false]], "multiassayexperiment.io.h5ad": [[2, "module-multiassayexperiment.io.h5ad", false]], "multiassayexperiment.io.interface": [[2, "module-multiassayexperiment.io.interface", false]], "multiassayexperiment.multiassayexperiment": [[1, "module-multiassayexperiment.MultiAssayExperiment", false]], "read_h5ad() (in module multiassayexperiment.io.h5ad)": [[2, "multiassayexperiment.io.h5ad.read_h5ad", false]], "replicated() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.replicated", false]], "rownames (multiassayexperiment.multiassayexperiment.multiassayexperiment property)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.rownames", false]], "sample_map (multiassayexperiment.multiassayexperiment.multiassayexperiment property)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.sample_map", false]], "sample_map (multiassayexperiment.multiassayexperiment.slicerresult attribute)": [[1, "multiassayexperiment.MultiAssayExperiment.SlicerResult.sample_map", false]], "set_column_data() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.set_column_data", false]], "set_experiment_names() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.set_experiment_names", false]], "set_experiments() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.set_experiments", false]], "set_metadata() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.set_metadata", false]], "set_sample_map() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.set_sample_map", false]], "slicerresult (class in multiassayexperiment.multiassayexperiment)": [[1, "multiassayexperiment.MultiAssayExperiment.SlicerResult", false]], "subset_by_column() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.subset_by_column", false]], "subset_by_experiments() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.subset_by_experiments", false]], "subset_by_row() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.subset_by_row", false]], "subset_experiments() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.subset_experiments", false]], "to_mudata() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.to_mudata", false]]}, "objects": {"": [[1, 0, 0, "-", "multiassayexperiment"]], "multiassayexperiment": [[1, 0, 0, "-", "MultiAssayExperiment"], [2, 0, 0, "-", "io"]], "multiassayexperiment.MultiAssayExperiment": [[1, 1, 1, "", "MultiAssayExperiment"], [1, 1, 1, "", "SlicerResult"]], "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment": [[1, 2, 1, "", "__copy__"], [1, 2, 1, "", "__deepcopy__"], [1, 2, 1, "", "__getitem__"], [1, 2, 1, "", "__repr__"], [1, 2, 1, "", "add_experiment"], [1, 3, 1, "", "assays"], [1, 3, 1, "", "colnames"], [1, 3, 1, "", "column_data"], [1, 3, 1, "", "column_names"], [1, 3, 1, "", "columnnames"], [1, 2, 1, "", "complete_cases"], [1, 2, 1, "", "copy"], [1, 2, 1, "", "experiment"], [1, 3, 1, "", "experiment_names"], [1, 3, 1, "", "experiments"], [1, 2, 1, "", "find_common_row_names"], [1, 2, 1, "", "from_anndata"], [1, 2, 1, "", "from_mudata"], [1, 2, 1, "", "get_column_data"], [1, 2, 1, "", "get_column_names"], [1, 2, 1, "", "get_experiment_names"], [1, 2, 1, "", "get_experiments"], [1, 2, 1, "", "get_metadata"], [1, 2, 1, "", "get_row_names"], [1, 2, 1, "", "get_sample_map"], [1, 2, 1, "", "get_with_column_data"], [1, 2, 1, "", "intersect_rows"], [1, 3, 1, "", "metadata"], [1, 2, 1, "", "replicated"], [1, 3, 1, "", "rownames"], [1, 3, 1, "", "sample_map"], [1, 2, 1, "", "set_column_data"], [1, 2, 1, "", "set_experiment_names"], [1, 2, 1, "", "set_experiments"], [1, 2, 1, "", "set_metadata"], [1, 2, 1, "", "set_sample_map"], [1, 2, 1, "", "subset_by_column"], [1, 2, 1, "", "subset_by_experiments"], [1, 2, 1, "", "subset_by_row"], [1, 2, 1, "", "subset_experiments"], [1, 2, 1, "", "to_mudata"]], "multiassayexperiment.MultiAssayExperiment.SlicerResult": [[1, 2, 1, "", "__getnewargs__"], [1, 2, 1, "", "__new__"], [1, 2, 1, "", "__repr__"], [1, 4, 1, "", "__slots__"], [1, 4, 1, "", "column_data"], [1, 4, 1, "", "experiments"], [1, 4, 1, "", "sample_map"]], "multiassayexperiment.io": [[2, 0, 0, "-", "h5ad"], [2, 0, 0, "-", "interface"]], "multiassayexperiment.io.h5ad": [[2, 5, 1, "", "read_h5ad"]], "multiassayexperiment.io.interface": [[2, 5, 1, "", "make_mae"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "method", "Python method"], "3": ["py", "property", "Python property"], "4": ["py", "attribute", "Python attribute"], "5": ["py", "function", "Python function"]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:method", "3": "py:property", "4": "py:attribute", "5": "py:function"}, "terms": {"": [1, 4, 5, 6, 8, 9], "0": [1, 5, 6, 8, 9], "1": [1, 5, 6, 8, 9], "10": [8, 9], "100": [8, 9], "1000": 8, "11": 8, "110": [8, 9], "12": 8, "150": 8, "2": [1, 5, 6, 8, 9], "20": [8, 9], "200": [8, 9], "2022": 7, "3": [5, 6, 8, 9], "300": [8, 9], "310": [8, 9], "4": [6, 8, 9], "5": [8, 9], "50": 8, "500kb": 5, "6": [8, 9], "7": 5, "8": 8, "8000": 5, "9": 8, "A": [1, 2, 4, 7, 8], "AND": 7, "AS": 7, "As": 4, "BE": [5, 7], "BUT": 7, "By": 5, "FOR": 7, "For": [5, 8, 9], "IN": 7, "IT": 5, "If": [1, 2, 5, 8], "In": [4, 5, 8], "It": [8, 9], "NO": 7, "NOT": 7, "OF": [5, 7], "OR": [5, 7], "One": 8, "THE": [5, 7], "TO": [5, 7], "The": [1, 2, 5, 7, 8, 9], "These": 8, "To": [6, 9], "WITH": 7, "_": [8, 9], "__copy__": [0, 1, 4], "__deepcopy__": [0, 1], "__getitem__": [0, 1, 4], "__getnewargs__": [0, 1], "__new__": [0, 1], "__repr__": [0, 1], "__slots__": [0, 1], "_build": 5, "_cl": 1, "_nil": 1, "abbrev": 5, "abl": 5, "about": [5, 8, 9], "abov": 7, "accept": 8, "access": [1, 4], "accident": 5, "accord": 5, "accordingli": 5, "account": 5, "acess": 1, "across": [1, 8], "action": 7, "activ": 5, "ad": [1, 5], "adata": 8, "adata2": 8, "add": [1, 2, 4, 5, 8], "add_experi": [0, 1], "addit": [1, 4, 5], "addition": 8, "after": 5, "aim": 8, "alia": 1, "all": [1, 2, 4, 5, 7, 8, 9], "allow": [4, 8], "along": 1, "alreadi": 5, "also": [4, 5, 8], "an": [1, 2, 4, 7, 9], "ani": [1, 2, 5, 7, 8, 9], "anndata": [1, 2], "annoi": 4, "anyth": [5, 8, 9], "api": 5, "appar": 8, "append": 1, "appli": 5, "appreci": 5, "approach": 8, "ar": [1, 2, 4, 5, 8], "arang": 8, "architectur": 5, "arg": 1, "aris": 7, "assai": [0, 1, 6, 8, 9], "associ": 7, "assum": 5, "assumpt": 5, "attribut": 8, "attributeerror": 1, "author": [5, 6, 7], "autom": 5, "automat": [5, 8], "av": 5, "avail": [5, 8], "avoid": 5, "b": 5, "back": [1, 8, 9], "base": [1, 4, 5, 8], "becaus": 8, "been": [4, 5, 9], "befor": [4, 5], "behavior": 5, "behind": 5, "being": 5, "best": 5, "big": 5, "bin": 5, "binari": 5, "bio": [8, 9], "biocfram": [1, 4, 8, 9], "bioconductor": [1, 6, 9], "biolog": [8, 9], "biosampl": [8, 9], "bitbucket": 5, "black": 5, "bool": 1, "boolean": [1, 8], "both": [4, 8], "bottom": 5, "branch": 5, "break": 5, "breakpoint": 5, "bring": 4, "browser": 5, "bug": 5, "bugfix": 5, "build": 5, "built": 5, "button": 5, "c": 7, "call": 8, "camelcas": 4, "can": [2, 4, 5, 8, 9], "case": [4, 5, 9], "caus": 5, "cd": 5, "cell": [1, 2, 8, 9], "cfg": 5, "changelog": 6, "charg": 7, "check": [1, 5, 8], "checkout": [1, 5, 9], "chip": [8, 9], "chr1": [8, 9], "chr2": [8, 9], "chr3": [8, 9], "ci": 5, "claim": 7, "class": [1, 4, 5, 6, 8, 9], "classmethod": 1, "clean": 5, "click": 5, "close": 5, "clutter": 5, "code": [4, 6], "coher": 5, "col_data": [1, 2, 8, 9], "col_data_s": [8, 9], "col_data_sc": [8, 9], "collabor": 5, "collect": 5, "colnam": [0, 1, 8, 9], "column": [1, 9], "column_data": [0, 1, 4, 8, 9], "column_nam": [0, 1, 4], "columnnam": [0, 1], "com": [3, 5], "come": 5, "command": 5, "commit": [4, 5], "common": [1, 8], "common_row": 8, "common_rows_ma": 8, "commonmark": 5, "commun": 5, "compani": 5, "compat": [1, 5], "compil": [4, 5], "complet": [4, 5], "complete_cas": [0, 1, 8], "complex": [4, 8], "concept": 5, "conda": 5, "condit": 7, "conduct": [5, 6, 8, 9], "configur": [4, 5], "confus": 5, "connect": 7, "consid": [1, 2, 5, 8], "consider": 5, "consist": [1, 4, 8], "construct": 6, "constructor": 8, "contain": [1, 4, 6, 8, 9], "content": [0, 5], "continu": 5, "contract": 7, "contribut": 6, "contributor": 5, "conveni": 8, "convert": [2, 4, 8], "copi": [0, 1, 5, 7, 8, 9], "copyright": 7, "correct": 5, "correctli": 5, "correspond": 8, "could": [8, 9], "count": [8, 9], "cov": 5, "creat": [1, 2, 4, 8, 9], "current": [1, 5], "d": 8, "d2": 8, "damag": 7, "data": [1, 8, 9], "datafram": 4, "deal": 7, "decid": 5, "decor": 5, "dedic": 5, "deep": 1, "default": [1, 4], "definit": 5, "depend": [4, 5, 8], "describ": 5, "descript": 5, "design": [5, 8], "detail": [5, 8, 9], "develop": [4, 5], "dict": [1, 2], "dictionari": [1, 2, 8], "differ": [5, 8, 9], "dimens": 1, "directori": 5, "dirti": 5, "discuss": [5, 8], "disk": 5, "dist": 5, "distribut": [5, 7], "do": [5, 7], "doc": [4, 5], "docstr": [4, 5], "document": [4, 6, 7, 8, 9], "doe": [1, 8], "doesn": 8, "don": [5, 8], "done": 5, "dot": 8, "doubt": 5, "downstream": 4, "draft": 5, "drop": 5, "dunder": 4, "duplic": 4, "dure": 8, "e": [4, 5], "each": [1, 2, 8, 9], "easi": 5, "easili": [5, 8], "edit": 5, "editor": 5, "egg": 5, "either": [1, 2, 5, 8, 9], "element": [1, 8], "empti": 4, "entiti": [8, 9], "error": 5, "especi": [4, 5], "etc": 4, "even": 5, "event": 7, "eventu": 5, "everi": 4, "everyth": 5, "exampl": 5, "excel": 5, "except": 1, "exist": 1, "expect": [2, 4, 5], "experi": [0, 1, 2, 4, 5, 6, 9], "experiment": [6, 8, 9], "experiment_nam": [0, 1, 2, 8], "explan": 5, "express": 7, "expt_with_sample_info": 8, "extend": [1, 8, 9], "extens": 5, "extern": 4, "extra": 5, "extract": 1, "f": [8, 9], "face": 5, "factor": 5, "fall": 5, "fals": [1, 8], "familiar": 5, "featur": [4, 5], "feedback": 5, "feel": 5, "fetch": 5, "few": [1, 5, 8, 9], "field": 1, "file": [2, 5, 7], "filter": [1, 8], "final": [8, 9], "find": [1, 5, 8], "find_common_row_nam": [0, 1, 8], "fine": 5, "finish": 5, "fire": 5, "first": [5, 8, 9], "fit": 7, "fix": 5, "flag": 5, "flake8": 5, "focu": 5, "focus": 5, "folder": 5, "follow": [1, 4, 5, 6, 7, 8, 9], "forget": 5, "fork": 5, "form": 5, "format": [1, 4], "foundat": 5, "free": [5, 7], "freecodecamp": 5, "freshli": 5, "from": [1, 2, 4, 5, 6, 7, 8, 9], "from_anndata": [0, 1, 2], "from_mudata": [0, 1, 8], "full": 8, "function": [1, 2, 4, 5, 6], "furnish": 7, "further": 8, "g": [4, 5], "gc": [8, 9], "genentech": 7, "gener": 5, "genom": [1, 6, 8, 9], "genomicrang": [8, 9], "gerrit": 5, "get": [1, 5, 6, 9], "get_column_data": [0, 1], "get_column_nam": [0, 1, 8], "get_experi": [0, 1], "get_experiment_nam": [0, 1, 8], "get_metadata": [0, 1], "get_row_nam": [0, 1, 8], "get_sample_map": [0, 1], "get_with_column_data": [0, 1, 8], "getter": 6, "git": 5, "github": 5, "gitlab": 5, "gmail": 3, "go": 5, "good": 5, "googl": 4, "gr": [8, 9], "grant": 7, "graph": 5, "greater": 1, "group": 5, "guid": [4, 5], "guidelin": 5, "h5ad": [0, 1], "ha": [4, 8, 9], "handi": 5, "hash": 5, "have": [1, 5, 8], "help": [5, 6], "helper": [4, 6], "herebi": 7, "highli": 5, "histori": 5, "hold": 5, "holder": 7, "hook": 5, "host": 5, "html": 5, "http": [5, 9], "i": [1, 2, 4, 5, 7, 8, 9], "icon": 5, "idea": 5, "identifi": [1, 5, 8], "ignor": 4, "illustr": 5, "implement": 8, "impli": 7, "import": [1, 2, 5, 8, 9], "importantli": 8, "improv": 6, "in_plac": [1, 8], "inc": 7, "includ": [5, 7, 8], "independ": [2, 8, 9], "index": [1, 4, 5, 6, 8, 9], "indexerror": 1, "indic": 1, "info": 5, "inform": [1, 5, 8, 9], "initi": 4, "input": [1, 8, 9], "instal": 5, "instanc": 1, "instead": [4, 5], "instruct": 5, "int": 1, "integ": 1, "integr": 5, "interact": 5, "interest": [5, 8], "interfac": [0, 1, 5, 8], "intern": 5, "intersect_row": [0, 1, 8], "intersphinx": 4, "io": [0, 1], "irang": [8, 9], "isback": 1, "isol": 5, "issu": 6, "item": 5, "its": [5, 8, 9], "j": 8, "jayaram": 3, "jkanch": 3, "just": 5, "k": [5, 8], "kancherla": 3, "keep": 1, "kei": [1, 2, 8], "kept": 5, "kind": [5, 7], "label": [5, 8, 9], "languag": 5, "last": 8, "least": 5, "len": 8, "length": 8, "let": [8, 9], "liabil": 7, "liabl": 7, "licens": 6, "like": 5, "limit": 7, "line": [8, 9], "link": [4, 5], "lint": 4, "list": [1, 5, 8, 9], "littl": 5, "loc": 8, "local": 5, "localhost": 5, "log": 5, "look": 5, "lot": 5, "m": 5, "machin": 5, "made": 5, "mae": [1, 2, 4, 6, 9], "mae_obj": 8, "mai": [1, 4, 5, 8, 9], "main": [5, 8, 9], "mainli": 8, "maintain": 6, "major": [4, 5], "make": 5, "make_ma": [1, 2], "manag": [1, 6, 8, 9], "mani": 1, "manual": 5, "map": [1, 2, 4, 9], "mark": 5, "markdown": 4, "markup": 5, "match": [8, 9], "matter": 8, "mcol": [8, 9], "mdata": 8, "mean": 5, "mechan": 5, "memo": 1, "mention": 5, "merchant": 7, "merg": [1, 5, 7], "messag": 5, "metadata": [0, 1, 8, 9], "method": [4, 5, 8], "might": [1, 5, 8], "migrat": 4, "mind": 5, "miniconda": 5, "minim": 5, "miss": 5, "mistak": 5, "mit": 7, "modal": 8, "mode": 1, "model": 5, "modif": 4, "modifi": [1, 5, 7], "modified_column_data": 8, "modified_ma": 8, "modul": [0, 5, 6, 8], "modulenotfounderror": 8, "more": [1, 4, 5, 8, 9], "moreov": 5, "most": 8, "motiv": 5, "mudata": 1, "multi": [1, 6, 9], "multiassayexperi": [5, 8], "multipl": [6, 9], "must": [1, 8, 9], "my": 5, "myst": [4, 5], "n": [5, 8], "n_ob": 8, "n_var": 8, "naiv": [1, 2, 8], "name": [1, 2, 4, 5, 9], "navig": 5, "ncol": [8, 9], "necess": 8, "need": [5, 8], "never": 5, "new": [1, 5], "nice": 1, "non": 5, "none": [1, 4, 8], "noninfring": 7, "normal": [5, 8], "normalize_subscript": 1, "notat": 8, "note": [4, 8], "notic": [5, 7], "now": [4, 8], "np": [8, 9], "nrow": [8, 9], "number": [1, 4, 8], "numpi": [8, 9], "object": [1, 2, 4, 8, 9], "obs_": 8, "obs_nam": 8, "obtain": 7, "occur": 5, "often": 5, "old": 5, "omic": [1, 6, 9], "onc": 5, "one": [4, 5, 8, 9], "onelin": 5, "onli": 8, "open": 5, "oper": [4, 5, 8], "option": [1, 5], "order": 5, "org": [5, 9], "origin": [1, 5, 8], "other": [5, 7, 8, 9], "otherwis": [7, 8], "our": [4, 8], "out": [5, 7, 8], "outcom": 8, "output": 9, "overview": 6, "packag": [0, 4, 5, 6, 9], "page": [5, 6], "palat": 4, "panda": 4, "paradigm": [4, 8], "paragraph": 5, "paramet": [1, 2, 4], "parser": 4, "part": [4, 5], "particular": 7, "pass": 5, "path": [2, 5], "patient": [8, 9], "pattern": [1, 2, 5, 8], "pdb": 5, "pencil": 5, "per": [8, 9], "perfectli": 5, "perform": [8, 9], "permiss": [5, 7], "permit": 7, "person": 7, "pickl": 1, "pip": [5, 6, 9], "pipx": 5, "place": 1, "plain": 1, "pleas": 5, "portion": 7, "posit": 1, "potenti": 5, "pprint": 8, "pr": 5, "pre": [4, 5], "present": [1, 8, 9], "pretti": [5, 8], "prevent": 8, "preview": 5, "previous": 5, "primari": [8, 9], "principl": 5, "print": 8, "privat": [4, 5], "problem": 5, "process": 5, "produc": 8, "program": 5, "project": [5, 9], "promot": 5, "properti": [1, 8], "propos": 5, "proprietari": 5, "provid": [1, 2, 4, 5, 7, 8, 9], "public": 5, "publicli": 5, "publish": [5, 7], "pull": 5, "purpos": 7, "push": 5, "pypi": [5, 6, 9], "pyscaffold": [4, 5, 9], "pytest": 5, "python": [4, 5], "python3": 5, "quick": 5, "quickli": 5, "quit": 5, "r": [1, 5, 6, 8, 9], "rais": [1, 2, 4], "rand": [8, 9], "random": [8, 9], "rang": [1, 8, 9], "rangedsummarizedexperi": [8, 9], "re": [5, 8], "read": [1, 2], "read_h5ad": [1, 2], "readabl": 5, "readi": 5, "reason": 5, "recent": 8, "recommend": [5, 8], "record": 5, "recreat": 5, "recur": 5, "reduc": 4, "refer": [1, 4, 5, 6], "reflect": [1, 2, 8], "releas": 4, "reliabl": 5, "remot": 5, "remov": [5, 8], "repl": 5, "replac": [1, 5], "replic": [0, 1], "report": 6, "repres": [1, 6, 8, 9], "represent": 1, "reproduc": 5, "reproduct": 5, "request": 5, "requir": 5, "resourc": 5, "respect": 5, "rest": 8, "restrict": 7, "restructuredtext": 5, "result": 8, "return": [1, 2, 5, 8], "review": 5, "rewrit": 4, "rf": 5, "rich": 8, "right": 7, "rm": 5, "rna": 8, "robust": 4, "root": 5, "routin": 4, "row": [1, 4, 9], "row_data": [8, 9], "row_nam": [8, 9], "rownam": [0, 1], "rst": [4, 5], "run": [4, 5], "sake": 8, "same": [1, 2, 5, 8], "sampl": [1, 2, 4, 9], "sample1": [8, 9], "sample2": [8, 9], "sample_data": [1, 8, 9], "sample_map": [0, 1, 2, 4, 8, 9], "scale": 8, "sce": [8, 9], "sce_": [8, 9], "sce_0": [8, 9], "sce_1": [8, 9], "sce_2": [8, 9], "sce_3": [8, 9], "sce_4": [8, 9], "sce_5": [8, 9], "score": [8, 9], "script": 5, "se": [8, 9], "se_": [8, 9], "se_0": [8, 9], "se_1": [8, 9], "se_2": [8, 9], "se_3": [8, 9], "se_4": [8, 9], "se_5": [8, 9], "search": [5, 6], "section": [5, 8], "see": [1, 5, 9], "seed": 8, "select": 8, "self": 1, "sell": 7, "send": 5, "seqnam": [8, 9], "sequenc": 1, "serv": 8, "server": 5, "servic": 5, "session": 5, "set": [1, 6, 8, 9], "set_column": 8, "set_column_data": [0, 1, 8], "set_experi": [0, 1], "set_experiment_nam": [0, 1], "set_metadata": [0, 1], "set_sample_map": [0, 1], "setter": 6, "setup": [4, 5], "setuptool": 5, "sever": 5, "shall": 7, "shallow": 1, "share": [6, 8, 9], "should": 5, "similar": 5, "simplifi": [5, 6, 8, 9], "sinc": 1, "singlecellexperi": [2, 8, 9], "six": 5, "size": [5, 8], "slice": [1, 4, 8], "slicerresult": [0, 1], "snake_cas": 4, "snippet": 4, "so": 7, "softwar": [5, 7], "sole": 8, "solut": 5, "solv": 5, "some": 4, "sometim": [4, 5], "sort": 5, "sourc": [1, 2, 5], "spatial": 8, "special": 4, "specif": 5, "specifi": 1, "specimen": [6, 8, 9], "sphinx": [4, 5], "src": 5, "start": [5, 6, 8, 9], "static": 1, "step": 5, "still": 5, "str": [1, 2], "strand": [8, 9], "streamlin": 4, "string": 1, "style": [4, 5, 8], "subclass": 2, "subject": [5, 7], "sublicens": 7, "submodul": 0, "subpackag": 0, "subset": [1, 4, 6], "subset_by_column": [0, 1], "subset_by_experi": [0, 1], "subset_by_row": [0, 1], "subset_experi": [0, 1], "subset_ma": 8, "substanti": 7, "success": 5, "summari": 5, "summarizedexperi": [1, 2, 8, 9], "suppos": 5, "sure": 5, "system": 5, "t": [5, 8], "tabl": [8, 9], "tag": 5, "task": [4, 6], "templat": 5, "term": 5, "terminologi": 5, "test": [4, 5], "text": 5, "than": 1, "thei": 5, "them": 5, "thi": [1, 2, 4, 5, 7, 8, 9], "thing": 5, "those": 8, "though": 5, "three": [8, 9], "tip": 5, "to_mudata": [0, 1], "to_panda": [8, 9], "too": [1, 5], "top": 5, "tort": 7, "tox": 5, "traceback": 8, "tracker": 5, "transform": 1, "treatment": [8, 9], "tricki": 5, "trivial": 5, "troubl": 5, "true": [1, 5, 8], "try": 5, "tsce": [8, 9], "tse2": [8, 9], "tupl": 1, "tutori": [4, 8], "txt": 5, "type": [1, 2, 4, 8], "typeerror": 2, "u": [4, 5], "uncom": 5, "under": 5, "unexpect": 8, "union": 1, "unit": [5, 8, 9], "unknown": 1, "unknown_sampl": 1, "unknown_sample_": [1, 2, 8], "unknown_sample_s": 8, "unknown_sample_sc": 8, "unnecessari": 5, "unwant": 5, "up": [5, 9], "updat": [4, 5], "upload": 5, "upon": 5, "upstream": 5, "url": 5, "us": [1, 2, 4, 5, 7, 8, 9], "user": 5, "v1": 5, "valid": [1, 5], "valu": [1, 2, 8], "valueerror": 1, "var2_": 8, "var_": 8, "var_nam": 8, "variou": 8, "vector": [1, 8], "venv": 5, "veri": 5, "verifi": 4, "version": [5, 6], "via": 5, "virtual": 5, "virtualenv": 5, "w": 8, "w2": 8, "wa": 5, "wai": 5, "want": 5, "warn": 4, "warranti": 7, "we": [1, 2, 5, 8, 9], "web": 5, "weird": 5, "welcom": 5, "well": 5, "what": 5, "when": 5, "where": [1, 8], "whether": [1, 7, 8], "which": [5, 8], "while": [4, 5, 8], "whom": 7, "why": 8, "with_sample_data": [1, 8], "within": [1, 8, 9], "without": 7, "wonder": 8, "work": 5, "workflow": 5, "would": 5, "write": 5, "written": 5, "x": 8, "y": 8, "y2": 8, "you": [5, 8], "yourlogin": 5, "yourself": 5, "z": 8}, "titles": ["multiassayexperiment", "multiassayexperiment package", "multiassayexperiment.io package", "Contributors", "Changelog", "Contributing", "MultiAssayExperiment", "License", "Multiple experiments", "MultiAssayExperiment"], "titleterms": {"0": 4, "1": 4, "2": 4, "3": 4, "4": 4, "No": 8, "access": 8, "accessor": 8, "an": [5, 8], "anndata": 8, "case": 8, "chang": 5, "changelog": 4, "clone": 5, "code": 5, "column": 8, "complet": 8, "construct": 8, "content": [1, 2, 6], "contribut": 5, "contributor": 3, "creat": 5, "dimens": 8, "document": 5, "empti": 8, "environ": 5, "experi": 8, "function": 8, "getter": 8, "h5ad": 2, "helper": 8, "implement": 5, "improv": 5, "indic": [6, 8], "instal": [6, 9], "interfac": 2, "interop": 8, "intersect": 8, "io": 2, "issu": 5, "licens": 7, "mae": 8, "maintain": 5, "map": 8, "modul": [1, 2], "mudata": 8, "multiassayexperi": [0, 1, 2, 6, 9], "multipl": 8, "name": 8, "note": 9, "packag": [1, 2], "releas": 5, "replic": 8, "report": 5, "repositori": 5, "row": 8, "sampl": 8, "setter": 8, "submit": 5, "submodul": [1, 2], "subpackag": 1, "subset": 8, "tabl": 6, "task": 5, "todo": 5, "troubleshoot": 5, "usag": 9, "version": 4, "your": 5}}) \ No newline at end of file +Search.setIndex({"alltitles": {"Access an experiment": [[8, "access-an-experiment"]], "Changelog": [[4, null]], "Clone the repository": [[5, "clone-the-repository"]], "Code Contributions": [[5, "code-contributions"]], "Complete cases": [[8, "complete-cases"]], "Construction": [[8, "construction"]], "Contents": [[6, "contents"]], "Contributing": [[5, "contributing"]], "Contributors": [[3, null]], "Create an environment": [[5, "create-an-environment"]], "Documentation Improvements": [[5, "documentation-improvements"]], "Empty MAE": [[8, "empty-mae"]], "Getters/Setters": [[8, "getters-setters"]], "Helper functions": [[8, "helper-functions"]], "Implement your changes": [[5, "implement-your-changes"]], "Indices and tables": [[6, "indices-and-tables"]], "Install": [[6, "install"], [9, "install"]], "Interop with anndata or mudata": [[8, "interop-with-anndata-or-mudata"]], "Intersect rows": [[8, "intersect-rows"]], "Issue Reports": [[5, "issue-reports"]], "License": [[7, null]], "Maintainer tasks": [[5, "maintainer-tasks"]], "Module contents": [[1, "module-multiassayexperiment"], [2, "module-multiassayexperiment.io"]], "MultiAssayExperiment": [[6, null], [9, null]], "Multiple experiments": [[8, null]], "No sample mapping?": [[8, "no-sample-mapping"]], "Note": [[9, "note"]], "Releases": [[5, "releases"]], "Replicates": [[8, "replicates"]], "Row or column name accessors": [[8, "row-or-column-name-accessors"]], "Setters": [[8, "setters"]], "Submit an issue": [[5, "submit-an-issue"]], "Submit your contribution": [[5, "submit-your-contribution"]], "Submodules": [[1, "submodules"], [2, "submodules"]], "Subpackages": [[1, "subpackages"]], "Subset by experiments dimension": [[8, "subset-by-experiments-dimension"]], "Subset by indices": [[8, "subset-by-indices"]], "Subsetting": [[8, "subsetting"]], "Todo": [[5, null], [5, "id2"], [5, "id3"], [5, "id5"], [5, "id6"], [5, "id7"], [5, "id8"], [5, "id9"], [5, "id10"], [5, "id11"], [5, "id12"]], "Troubleshooting": [[5, "troubleshooting"]], "Usage": [[9, "usage"]], "Version 0.1": [[4, "version-0-1"]], "Version 0.2.0": [[4, "version-0-2-0"]], "Version 0.3.0": [[4, "version-0-3-0"]], "Version 0.4.0": [[4, "version-0-4-0"]], "Version 0.4.1 - 0.4.3": [[4, "version-0-4-1-0-4-3"]], "Version 0.5.0": [[4, "version-0-5-0"]], "multiassayexperiment": [[0, null]], "multiassayexperiment package": [[1, null]], "multiassayexperiment.MultiAssayExperiment module": [[1, "module-multiassayexperiment.MultiAssayExperiment"]], "multiassayexperiment.io package": [[2, null]], "multiassayexperiment.io.h5ad module": [[2, "module-multiassayexperiment.io.h5ad"]], "multiassayexperiment.io.interface module": [[2, "module-multiassayexperiment.io.interface"]]}, "docnames": ["api/modules", "api/multiassayexperiment", "api/multiassayexperiment.io", "authors", "changelog", "contributing", "index", "license", "overview", "readme"], "envversion": {"sphinx": 64, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1}, "filenames": ["api/modules.rst", "api/multiassayexperiment.rst", "api/multiassayexperiment.io.rst", "authors.md", "changelog.md", "contributing.md", "index.md", "license.md", "overview.md", "readme.md"], "indexentries": {"__copy__() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.__copy__", false]], "__deepcopy__() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.__deepcopy__", false]], "__getitem__() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.__getitem__", false]], "__getnewargs__() (multiassayexperiment.multiassayexperiment.slicerresult method)": [[1, "multiassayexperiment.MultiAssayExperiment.SlicerResult.__getnewargs__", false]], "__match_args__ (multiassayexperiment.multiassayexperiment.slicerresult attribute)": [[1, "multiassayexperiment.MultiAssayExperiment.SlicerResult.__match_args__", false]], "__new__() (multiassayexperiment.multiassayexperiment.slicerresult static method)": [[1, "multiassayexperiment.MultiAssayExperiment.SlicerResult.__new__", false]], "__repr__() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.__repr__", false]], "__repr__() (multiassayexperiment.multiassayexperiment.slicerresult method)": [[1, "multiassayexperiment.MultiAssayExperiment.SlicerResult.__repr__", false]], "__slots__ (multiassayexperiment.multiassayexperiment.slicerresult attribute)": [[1, "multiassayexperiment.MultiAssayExperiment.SlicerResult.__slots__", false]], "add_experiment() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.add_experiment", false]], "assays (multiassayexperiment.multiassayexperiment.multiassayexperiment property)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.assays", false]], "colnames (multiassayexperiment.multiassayexperiment.multiassayexperiment property)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.colnames", false]], "column_data (multiassayexperiment.multiassayexperiment.multiassayexperiment property)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.column_data", false]], "column_data (multiassayexperiment.multiassayexperiment.slicerresult attribute)": [[1, "multiassayexperiment.MultiAssayExperiment.SlicerResult.column_data", false]], "column_names (multiassayexperiment.multiassayexperiment.multiassayexperiment property)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.column_names", false]], "columnnames (multiassayexperiment.multiassayexperiment.multiassayexperiment property)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.columnnames", false]], "complete_cases() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.complete_cases", false]], "copy() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.copy", false]], "experiment() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.experiment", false]], "experiment_names (multiassayexperiment.multiassayexperiment.multiassayexperiment property)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.experiment_names", false]], "experiments (multiassayexperiment.multiassayexperiment.multiassayexperiment property)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.experiments", false]], "experiments (multiassayexperiment.multiassayexperiment.slicerresult attribute)": [[1, "multiassayexperiment.MultiAssayExperiment.SlicerResult.experiments", false]], "find_common_row_names() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.find_common_row_names", false]], "from_anndata() (multiassayexperiment.multiassayexperiment.multiassayexperiment class method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.from_anndata", false]], "from_mudata() (multiassayexperiment.multiassayexperiment.multiassayexperiment class method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.from_mudata", false]], "get_column_data() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.get_column_data", false]], "get_column_names() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.get_column_names", false]], "get_experiment_names() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.get_experiment_names", false]], "get_experiments() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.get_experiments", false]], "get_metadata() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.get_metadata", false]], "get_row_names() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.get_row_names", false]], "get_sample_map() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.get_sample_map", false]], "get_with_column_data() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.get_with_column_data", false]], "intersect_rows() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.intersect_rows", false]], "make_mae() (in module multiassayexperiment.io.interface)": [[2, "multiassayexperiment.io.interface.make_mae", false]], "metadata (multiassayexperiment.multiassayexperiment.multiassayexperiment property)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.metadata", false]], "module": [[1, "module-multiassayexperiment", false], [1, "module-multiassayexperiment.MultiAssayExperiment", false], [2, "module-multiassayexperiment.io", false], [2, "module-multiassayexperiment.io.h5ad", false], [2, "module-multiassayexperiment.io.interface", false]], "multiassayexperiment": [[1, "module-multiassayexperiment", false]], "multiassayexperiment (class in multiassayexperiment.multiassayexperiment)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment", false]], "multiassayexperiment.io": [[2, "module-multiassayexperiment.io", false]], "multiassayexperiment.io.h5ad": [[2, "module-multiassayexperiment.io.h5ad", false]], "multiassayexperiment.io.interface": [[2, "module-multiassayexperiment.io.interface", false]], "multiassayexperiment.multiassayexperiment": [[1, "module-multiassayexperiment.MultiAssayExperiment", false]], "read_h5ad() (in module multiassayexperiment.io.h5ad)": [[2, "multiassayexperiment.io.h5ad.read_h5ad", false]], "replicated() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.replicated", false]], "rownames (multiassayexperiment.multiassayexperiment.multiassayexperiment property)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.rownames", false]], "sample_map (multiassayexperiment.multiassayexperiment.multiassayexperiment property)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.sample_map", false]], "sample_map (multiassayexperiment.multiassayexperiment.slicerresult attribute)": [[1, "multiassayexperiment.MultiAssayExperiment.SlicerResult.sample_map", false]], "set_column_data() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.set_column_data", false]], "set_experiment_names() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.set_experiment_names", false]], "set_experiments() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.set_experiments", false]], "set_metadata() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.set_metadata", false]], "set_sample_map() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.set_sample_map", false]], "slicerresult (class in multiassayexperiment.multiassayexperiment)": [[1, "multiassayexperiment.MultiAssayExperiment.SlicerResult", false]], "subset_by_column() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.subset_by_column", false]], "subset_by_experiments() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.subset_by_experiments", false]], "subset_by_row() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.subset_by_row", false]], "subset_experiments() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.subset_experiments", false]], "to_mudata() (multiassayexperiment.multiassayexperiment.multiassayexperiment method)": [[1, "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.to_mudata", false]]}, "objects": {"": [[1, 0, 0, "-", "multiassayexperiment"]], "multiassayexperiment": [[1, 0, 0, "-", "MultiAssayExperiment"], [2, 0, 0, "-", "io"]], "multiassayexperiment.MultiAssayExperiment": [[1, 1, 1, "", "MultiAssayExperiment"], [1, 1, 1, "", "SlicerResult"]], "multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment": [[1, 2, 1, "", "__copy__"], [1, 2, 1, "", "__deepcopy__"], [1, 2, 1, "", "__getitem__"], [1, 2, 1, "", "__repr__"], [1, 2, 1, "", "add_experiment"], [1, 3, 1, "", "assays"], [1, 3, 1, "", "colnames"], [1, 3, 1, "", "column_data"], [1, 3, 1, "", "column_names"], [1, 3, 1, "", "columnnames"], [1, 2, 1, "", "complete_cases"], [1, 2, 1, "", "copy"], [1, 2, 1, "", "experiment"], [1, 3, 1, "", "experiment_names"], [1, 3, 1, "", "experiments"], [1, 2, 1, "", "find_common_row_names"], [1, 2, 1, "", "from_anndata"], [1, 2, 1, "", "from_mudata"], [1, 2, 1, "", "get_column_data"], [1, 2, 1, "", "get_column_names"], [1, 2, 1, "", "get_experiment_names"], [1, 2, 1, "", "get_experiments"], [1, 2, 1, "", "get_metadata"], [1, 2, 1, "", "get_row_names"], [1, 2, 1, "", "get_sample_map"], [1, 2, 1, "", "get_with_column_data"], [1, 2, 1, "", "intersect_rows"], [1, 3, 1, "", "metadata"], [1, 2, 1, "", "replicated"], [1, 3, 1, "", "rownames"], [1, 3, 1, "", "sample_map"], [1, 2, 1, "", "set_column_data"], [1, 2, 1, "", "set_experiment_names"], [1, 2, 1, "", "set_experiments"], [1, 2, 1, "", "set_metadata"], [1, 2, 1, "", "set_sample_map"], [1, 2, 1, "", "subset_by_column"], [1, 2, 1, "", "subset_by_experiments"], [1, 2, 1, "", "subset_by_row"], [1, 2, 1, "", "subset_experiments"], [1, 2, 1, "", "to_mudata"]], "multiassayexperiment.MultiAssayExperiment.SlicerResult": [[1, 2, 1, "", "__getnewargs__"], [1, 4, 1, "", "__match_args__"], [1, 2, 1, "", "__new__"], [1, 2, 1, "", "__repr__"], [1, 4, 1, "", "__slots__"], [1, 4, 1, "", "column_data"], [1, 4, 1, "", "experiments"], [1, 4, 1, "", "sample_map"]], "multiassayexperiment.io": [[2, 0, 0, "-", "h5ad"], [2, 0, 0, "-", "interface"]], "multiassayexperiment.io.h5ad": [[2, 5, 1, "", "read_h5ad"]], "multiassayexperiment.io.interface": [[2, 5, 1, "", "make_mae"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "method", "Python method"], "3": ["py", "property", "Python property"], "4": ["py", "attribute", "Python attribute"], "5": ["py", "function", "Python function"]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:method", "3": "py:property", "4": "py:attribute", "5": "py:function"}, "terms": {"": [1, 4, 5, 6, 8, 9], "0": [1, 5, 6, 8, 9], "1": [1, 5, 6, 8, 9], "10": [8, 9], "100": [8, 9], "1000": 8, "11": 8, "110": [8, 9], "12": 8, "1429": 8, "150": 8, "1531": 8, "2": [1, 5, 6, 8, 9], "20": [8, 9], "200": [8, 9], "2022": 7, "3": [5, 6, 8, 9], "300": [8, 9], "310": [8, 9], "4": [6, 8, 9], "5": [6, 8, 9], "50": 8, "500kb": 5, "6": [8, 9], "7": 5, "8": [4, 8], "8000": 5, "9": 8, "A": [1, 2, 4, 7, 8], "AND": 7, "AS": 7, "As": 4, "BE": [5, 7], "BUT": 7, "By": 5, "FOR": 7, "For": [5, 8, 9], "IN": 7, "IT": 5, "If": [1, 2, 5, 8], "In": [4, 5, 8], "It": [8, 9], "NO": 7, "NOT": 7, "OF": [5, 7], "OR": [5, 7], "One": 8, "THE": [5, 7], "TO": [5, 7], "The": [1, 2, 5, 7, 8, 9], "These": 8, "To": [6, 9], "WITH": 7, "_": [8, 9], "__copy__": [0, 1, 4], "__deepcopy__": [0, 1], "__getitem__": [0, 1, 4], "__getnewargs__": [0, 1], "__match_args__": [0, 1], "__new__": [0, 1], "__repr__": [0, 1], "__slots__": [0, 1], "_build": 5, "_cl": 1, "_core": 8, "_nil": 1, "_update_attr": 8, "abbrev": 5, "abl": 5, "about": [5, 8, 9], "abov": 7, "accept": 8, "access": [1, 4], "accident": 5, "accord": 5, "accordingli": 5, "account": 5, "acess": 1, "across": [1, 8], "action": 7, "activ": 5, "ad": [1, 5], "adata": 8, "adata2": 8, "add": [1, 2, 4, 5, 8], "add_experi": [0, 1], "addit": [1, 4, 5], "addition": 8, "adopt": 8, "after": 5, "aim": 8, "alia": 1, "all": [1, 2, 4, 5, 7, 8, 9], "allow": [4, 8], "along": 1, "alreadi": 5, "also": [4, 5, 8], "an": [1, 2, 4, 7, 9], "ani": [1, 2, 5, 7, 8, 9], "anndata": [1, 2], "annoi": 4, "anymor": 8, "anyth": [5, 8, 9], "api": 5, "appar": 8, "append": 1, "appli": 5, "appreci": 5, "approach": 8, "ar": [1, 2, 4, 5, 8], "arang": 8, "architectur": 5, "arg": 1, "aris": 7, "assai": [0, 1, 6, 8, 9], "associ": 7, "assum": 5, "assumpt": 5, "attribut": 8, "attributeerror": 1, "author": [5, 6, 7], "autom": 5, "automat": [5, 8], "av": 5, "avail": [5, 8], "avoid": 5, "axi": 8, "b": 5, "back": [1, 8, 9], "base": [1, 4, 5, 8], "becaus": 8, "becom": 8, "been": [4, 5, 9], "befor": [4, 5], "behavior": 5, "behaviour": 8, "behind": 5, "being": 5, "best": 5, "big": 5, "bin": 5, "binari": 5, "bio": [8, 9], "biocfram": [1, 4, 8, 9], "bioconductor": [1, 6, 9], "biolog": [8, 9], "biosampl": [8, 9], "bitbucket": 5, "black": 5, "bool": 1, "boolean": [1, 8], "both": [4, 8], "bottom": 5, "branch": 5, "break": 5, "breakpoint": 5, "bring": 4, "browser": 5, "bug": 5, "bugfix": 5, "build": 5, "built": 5, "button": 5, "c": 7, "call": 8, "camelcas": 4, "can": [2, 4, 5, 8, 9], "case": [4, 5, 9], "caus": 5, "cd": 5, "cell": [1, 2, 8, 9], "cfg": 5, "changelog": 6, "charg": 7, "check": [1, 5, 8], "checkout": [1, 5, 9], "chip": [8, 9], "chore": 4, "chr1": [8, 9], "chr2": [8, 9], "chr3": [8, 9], "ci": 5, "claim": 7, "class": [1, 4, 5, 6, 8, 9], "classmethod": 1, "clean": 5, "click": 5, "close": 5, "clutter": 5, "code": [4, 6], "coher": 5, "col_data": [1, 2, 8, 9], "col_data_s": [8, 9], "col_data_sc": [8, 9], "collabor": 5, "collect": 5, "colnam": [0, 1, 8, 9], "column": [1, 9], "column_data": [0, 1, 4, 8, 9], "column_nam": [0, 1, 4], "columnnam": [0, 1], "com": [3, 5], "come": 5, "command": 5, "commit": [4, 5], "common": [1, 8], "common_row": 8, "common_rows_ma": 8, "commonmark": 5, "commun": 5, "compani": 5, "compat": [1, 5], "compil": [4, 5], "complet": [4, 5], "complete_cas": [0, 1, 8], "complex": [4, 8], "concept": 5, "conda": 5, "condit": 7, "conduct": [5, 6, 8, 9], "configur": [4, 5], "confus": 5, "connect": 7, "consid": [1, 2, 5, 8], "consider": 5, "consist": [1, 4, 8], "construct": 6, "constructor": 8, "contain": [1, 4, 6, 8, 9], "content": [0, 5], "continu": 5, "contract": 7, "contribut": 6, "contributor": 5, "conveni": 8, "convert": [2, 4, 8], "copi": [0, 1, 5, 7, 8, 9], "copyright": 7, "correct": 5, "correctli": 5, "correspond": 8, "could": [8, 9], "count": [8, 9], "cov": 5, "creat": [1, 2, 4, 8, 9], "current": [1, 5], "d": 8, "d2": 8, "damag": 7, "data": [1, 8, 9], "datafram": 4, "deal": 7, "decid": 5, "decor": 5, "dedic": 5, "deep": 1, "default": [1, 4, 8], "definit": 5, "depend": [4, 5, 8], "describ": 5, "descript": 5, "design": [5, 8], "detail": [5, 8, 9], "develop": [4, 5], "dict": [1, 2], "dictionari": [1, 2, 8], "differ": [5, 8, 9], "dimens": 1, "directori": 5, "dirti": 5, "discuss": [5, 8], "disk": 5, "dist": 5, "distribut": [5, 7], "do": [5, 7], "doc": [4, 5, 8], "docformatt": 4, "docstr": [4, 5], "document": [4, 6, 7, 8, 9], "doe": [1, 8], "doesn": 8, "don": [5, 8], "done": 5, "dot": 8, "doubt": 5, "downstream": 4, "draft": 5, "drop": 5, "dunder": 4, "duplic": 4, "dure": 8, "e": [4, 5], "each": [1, 2, 8, 9], "easi": 5, "easili": [5, 8], "edit": 5, "editor": 5, "egg": 5, "either": [1, 2, 5, 8, 9], "element": [1, 8], "empti": 4, "entiti": [8, 9], "eol": 4, "error": 5, "especi": [4, 5], "etc": 4, "even": 5, "event": 7, "eventu": 5, "everi": 4, "everyth": 5, "exampl": 5, "excel": 5, "except": 1, "exist": 1, "expect": [2, 4, 5], "experi": [0, 1, 2, 4, 5, 6, 9], "experiment": [6, 8, 9], "experiment_nam": [0, 1, 2, 8], "explan": 5, "express": 7, "expt_with_sample_info": 8, "extend": [1, 8, 9], "extens": 5, "extern": 4, "extra": 5, "extract": 1, "f": [8, 9], "face": 5, "factor": 5, "fall": 5, "fals": [1, 8], "familiar": 5, "featur": [4, 5], "feedback": 5, "feel": 5, "fetch": 5, "few": [1, 5, 8, 9], "field": 1, "file": [2, 5, 7], "filter": [1, 8], "final": [8, 9], "find": [1, 5, 8], "find_common_row_nam": [0, 1, 8], "fine": 5, "finish": 5, "fire": 5, "first": [5, 8, 9], "fit": 7, "fix": 5, "flag": 5, "flake8": 5, "flexibl": 8, "focu": 5, "focus": 5, "folder": 5, "follow": [1, 4, 5, 6, 7, 8, 9], "forget": 5, "fork": 5, "form": 5, "format": [1, 4], "formatt": 4, "foundat": 5, "free": [5, 7], "freecodecamp": 5, "freshli": 5, "from": [1, 2, 4, 5, 6, 7, 8, 9], "from_anndata": [0, 1, 2], "from_mudata": [0, 1, 8], "full": 8, "function": [1, 2, 4, 5, 6], "furnish": 7, "further": 8, "futurewarn": 8, "g": [4, 5], "gc": [8, 9], "genentech": 7, "gener": 5, "genom": [1, 6, 8, 9], "genomicrang": [8, 9], "gerrit": 5, "get": [1, 5, 6, 9], "get_column_data": [0, 1], "get_column_nam": [0, 1, 8], "get_experi": [0, 1], "get_experiment_nam": [0, 1, 8], "get_metadata": [0, 1], "get_row_nam": [0, 1, 8], "get_sample_map": [0, 1], "get_with_column_data": [0, 1, 8], "getter": 6, "git": 5, "github": 5, "gitlab": 5, "gmail": 3, "go": 5, "good": 5, "googl": 4, "gr": [8, 9], "grant": 7, "graph": 5, "greater": 1, "group": 5, "guid": [4, 5], "guidelin": 5, "h5ad": [0, 1], "ha": [4, 8, 9], "handi": 5, "hash": 5, "have": [1, 5, 8], "help": [5, 6], "helper": [4, 6], "herebi": 7, "highli": 5, "histori": 5, "hold": 5, "holder": 7, "home": 8, "hook": 5, "host": 5, "html": 5, "http": [5, 9], "i": [1, 2, 4, 5, 7, 8, 9], "icon": 5, "idea": 5, "identifi": [1, 5, 8], "ignor": 4, "illustr": 5, "implement": 8, "impli": 7, "import": [1, 2, 5, 8, 9], "importantli": 8, "improv": 6, "in_plac": [1, 8], "inc": 7, "includ": [5, 7, 8], "independ": [2, 8, 9], "index": [1, 4, 5, 6, 8, 9], "indexerror": 1, "indic": 1, "individu": 8, "info": 5, "inform": [1, 5, 8, 9], "initi": 4, "input": [1, 8, 9], "instal": 5, "instanc": 1, "instead": [4, 5], "instruct": 5, "int": 1, "integ": 1, "integr": 5, "interact": 5, "interest": [5, 8], "interfac": [0, 1, 5, 8], "intern": 5, "intersect_row": [0, 1, 8], "intersphinx": 4, "io": [0, 1], "irang": [8, 9], "isback": 1, "isol": 5, "issu": 6, "item": 5, "its": [5, 8, 9], "j": 8, "jayaram": 3, "jkanch": 3, "join_common": 8, "just": 5, "k": [5, 8], "kancherla": 3, "keep": 1, "kei": [1, 2, 8], "kept": 5, "kind": [5, 7], "label": [5, 8, 9], "languag": 5, "last": 8, "least": 5, "len": 8, "length": 8, "let": [8, 9], "liabil": 7, "liabl": 7, "lib": 8, "licens": 6, "like": 5, "limit": 7, "line": [8, 9], "link": [4, 5], "lint": 4, "list": [1, 5, 8, 9], "littl": 5, "loc": 8, "local": 5, "localhost": 5, "log": 5, "look": 5, "lot": 5, "m": 5, "machin": 5, "made": 5, "mae": [1, 2, 4, 6, 9], "mae_obj": 8, "mai": [1, 4, 5, 8, 9], "main": [5, 8, 9], "mainli": 8, "maintain": 6, "major": [4, 5], "make": 5, "make_ma": [1, 2], "manag": [1, 6, 8, 9], "mani": 1, "manual": 5, "map": [1, 2, 4, 9], "mark": 5, "markdown": 4, "markup": 5, "match": [8, 9], "matter": 8, "mcol": [8, 9], "mdata": 8, "mean": 5, "mechan": 5, "memo": 1, "mention": 5, "merchant": 7, "merg": [1, 5, 7], "messag": 5, "metadata": [0, 1, 8, 9], "method": [4, 5, 8], "might": [1, 5, 8], "migrat": 4, "mind": 5, "miniconda": 5, "minim": 5, "miss": 5, "mistak": 5, "mit": 7, "modal": 8, "mode": 1, "model": 5, "modif": 4, "modifi": [1, 5, 7], "modified_column_data": 8, "modified_ma": 8, "modul": [0, 5, 6, 8], "modulenotfounderror": 8, "more": [1, 4, 5, 8, 9], "moreov": 5, "most": 8, "motiv": 5, "mudata": 1, "multi": [1, 6, 9], "multiassayexperi": [5, 8], "multipl": [6, 9], "must": [1, 8, 9], "my": 5, "myst": [4, 5], "n": [5, 8], "n_ob": 8, "n_var": 8, "naiv": [1, 2, 8], "name": [1, 2, 4, 5, 9], "navig": 5, "ncol": [8, 9], "necess": 8, "need": [5, 8], "never": 5, "new": [1, 5, 8], "nice": 1, "non": 5, "none": [1, 4, 8], "noninfring": 7, "normal": [5, 8], "normalize_subscript": 1, "notat": 8, "note": [4, 8], "notic": [5, 7], "now": [4, 8], "np": [8, 9], "nrow": [8, 9], "number": [1, 4, 8], "numpi": [8, 9], "ob": 8, "object": [1, 2, 4, 8, 9], "obs_": 8, "obs_nam": 8, "obtain": 7, "occur": 5, "often": 5, "old": 5, "omic": [1, 6, 9], "onc": 5, "one": [4, 5, 8, 9], "onelin": 5, "onli": 8, "open": 5, "oper": [4, 5, 8], "option": [1, 5], "order": 5, "org": [5, 9], "origin": [1, 5, 8], "other": [5, 7, 8, 9], "otherwis": [7, 8], "our": [4, 8], "out": [5, 7, 8], "outcom": 8, "output": 9, "overview": 6, "packag": [0, 4, 5, 6, 8, 9], "page": [5, 6], "palat": 4, "panda": 4, "paradigm": [4, 8], "paragraph": 5, "paramet": [1, 2, 4], "parser": 4, "part": [4, 5], "particular": 7, "pass": 5, "path": [2, 5], "patient": [8, 9], "pattern": [1, 2, 5, 8], "pdb": 5, "pencil": 5, "per": [8, 9], "perfectli": 5, "perform": [8, 9], "permiss": [5, 7], "permit": 7, "person": 7, "pickl": 1, "pip": [5, 6, 9], "pipx": 5, "place": 1, "plain": 1, "pleas": 5, "portion": 7, "posit": 1, "potenti": 5, "pprint": 8, "pr": 5, "pre": [4, 5], "precommit": 4, "present": [1, 8, 9], "pretti": [5, 8], "prevent": 8, "preview": 5, "previous": 5, "primari": [8, 9], "principl": 5, "print": 8, "privat": [4, 5], "problem": 5, "process": 5, "produc": 8, "program": 5, "project": [5, 9], "promot": 5, "properti": [1, 8], "propos": 5, "proprietari": 5, "provid": [1, 2, 4, 5, 7, 8, 9], "public": 5, "publicli": 5, "publish": [5, 7], "pull": [5, 8], "pull_ob": 8, "pull_on_upd": 8, "pull_var": 8, "purpos": 7, "push": 5, "push_ob": 8, "push_var": 8, "py": 8, "pypi": [5, 6, 9], "pyscaffold": [4, 5, 9], "pytest": 5, "python": [4, 5], "python3": [5, 8], "quick": 5, "quickli": 5, "quit": 5, "r": [1, 5, 6, 8, 9], "rais": [1, 2, 4], "rand": [8, 9], "random": [8, 9], "rang": [1, 8, 9], "rangedsummarizedexperi": [8, 9], "re": [5, 8], "read": [1, 2], "read_h5ad": [1, 2], "readabl": 5, "readi": 5, "reason": 5, "recent": 8, "recommend": [5, 8], "record": 5, "recreat": 5, "recur": 5, "reduc": 4, "refer": [1, 4, 5, 6], "reflect": [1, 2, 8], "releas": 4, "reliabl": 5, "remot": 5, "remov": [4, 5, 8], "repl": 5, "replac": [1, 4, 5], "replic": [0, 1], "report": 6, "repres": [1, 6, 8, 9], "represent": 1, "reproduc": 5, "reproduct": 5, "request": 5, "requir": 5, "resourc": 5, "respect": 5, "rest": 8, "restrict": 7, "restructuredtext": 5, "result": 8, "return": [1, 2, 5, 8], "review": 5, "rewrit": 4, "rf": 5, "rich": 8, "right": 7, "rm": 5, "rna": 8, "robust": 4, "root": 5, "routin": 4, "row": [1, 4, 9], "row_data": [8, 9], "row_nam": [8, 9], "rownam": [0, 1], "rst": [4, 5], "ruff": 4, "run": [4, 5], "runner": 8, "sake": 8, "same": [1, 2, 5, 8], "sampl": [1, 2, 4, 9], "sample1": [8, 9], "sample2": [8, 9], "sample_data": [1, 8, 9], "sample_map": [0, 1, 2, 4, 8, 9], "scale": 8, "sce": [8, 9], "sce_": [8, 9], "sce_0": [8, 9], "sce_1": [8, 9], "sce_2": [8, 9], "sce_3": [8, 9], "sce_4": [8, 9], "sce_5": [8, 9], "score": [8, 9], "script": 5, "se": [8, 9], "se_": [8, 9], "se_0": [8, 9], "se_1": [8, 9], "se_2": [8, 9], "se_3": [8, 9], "se_4": [8, 9], "se_5": [8, 9], "search": [5, 6], "section": [5, 8], "see": [1, 5, 9], "seed": 8, "select": 8, "self": [1, 8], "sell": 7, "send": 5, "seqnam": [8, 9], "sequenc": 1, "serv": 8, "server": 5, "servic": 5, "session": 5, "set": [1, 6, 8, 9], "set_column": 8, "set_column_data": [0, 1, 8], "set_experi": [0, 1], "set_experiment_nam": [0, 1], "set_metadata": [0, 1], "set_opt": 8, "set_sample_map": [0, 1], "setter": 6, "setup": [4, 5], "setuptool": 5, "sever": 5, "shall": 7, "shallow": 1, "share": [6, 8, 9], "should": 5, "similar": 5, "simplifi": [5, 6, 8, 9], "sinc": 1, "singlecellexperi": [2, 8, 9], "site": 8, "six": 5, "size": [5, 8], "slice": [1, 4, 8], "slicerresult": [0, 1], "snake_cas": 4, "snippet": 4, "so": 7, "softwar": [5, 7], "sole": 8, "solut": 5, "solv": 5, "some": 4, "sometim": [4, 5], "sort": 5, "sourc": [1, 2, 5], "spatial": 8, "special": 4, "specif": 5, "specifi": 1, "specimen": [6, 8, 9], "sphinx": [4, 5], "src": 5, "start": [5, 6, 8, 9], "static": 1, "step": 5, "still": 5, "str": [1, 2], "strand": [8, 9], "streamlin": 4, "string": 1, "style": [4, 5, 8], "subclass": 2, "subject": [5, 7], "sublicens": 7, "submodul": 0, "subpackag": 0, "subset": [1, 4, 6], "subset_by_column": [0, 1], "subset_by_experi": [0, 1], "subset_by_row": [0, 1], "subset_experi": [0, 1], "subset_ma": 8, "substanti": 7, "success": 5, "summari": 5, "summarizedexperi": [1, 2, 8, 9], "suppos": 5, "sure": 5, "system": 5, "t": [5, 8], "tabl": [8, 9], "tag": 5, "task": [4, 6], "templat": 5, "term": 5, "terminologi": 5, "test": [4, 5], "text": 5, "than": 1, "thei": 5, "them": 5, "thi": [1, 2, 4, 5, 7, 8, 9], "thing": 5, "those": 8, "though": 5, "three": [8, 9], "tip": 5, "to_mudata": [0, 1], "to_panda": [8, 9], "too": [1, 5], "top": 5, "tort": 7, "tox": [5, 8], "traceback": 8, "tracker": 5, "transform": 1, "treatment": [8, 9], "tricki": 5, "trivial": 5, "troubl": 5, "true": [1, 5, 8], "try": 5, "tsce": [8, 9], "tse2": [8, 9], "tupl": 1, "tutori": [4, 8], "txt": 5, "type": [1, 2, 4, 8], "typeerror": 2, "u": [4, 5], "uncom": 5, "under": 5, "unexpect": 8, "union": 1, "unit": [5, 8, 9], "unknown": 1, "unknown_sampl": 1, "unknown_sample_": [1, 2, 8], "unknown_sample_s": 8, "unknown_sample_sc": 8, "unnecessari": 5, "unwant": 5, "up": [5, 9], "updat": [4, 5, 8], "upload": 5, "upon": 5, "upstream": 5, "url": 5, "us": [1, 2, 4, 5, 7, 8, 9], "user": 5, "v1": 5, "valid": [1, 5], "valu": [1, 2, 8], "valueerror": 1, "var": 8, "var2_": 8, "var_": 8, "var_nam": 8, "variou": 8, "vector": [1, 8], "venv": 5, "veri": 5, "verifi": 4, "version": [5, 6], "via": 5, "virtual": 5, "virtualenv": 5, "w": 8, "w2": 8, "wa": 5, "wai": 5, "want": 5, "warn": 4, "warranti": 7, "we": [1, 2, 5, 8, 9], "web": 5, "weird": 5, "welcom": 5, "well": 5, "what": 5, "when": 5, "where": [1, 8], "whether": [1, 7, 8], "which": [5, 8], "while": [4, 5, 8], "whom": 7, "why": 8, "with_sample_data": [1, 8], "within": [1, 8, 9], "without": 7, "wonder": 8, "work": [5, 8], "workflow": 5, "would": 5, "write": 5, "written": 5, "x": 8, "y": 8, "y2": 8, "you": [5, 8], "yourlogin": 5, "yourself": 5, "z": 8}, "titles": ["multiassayexperiment", "multiassayexperiment package", "multiassayexperiment.io package", "Contributors", "Changelog", "Contributing", "MultiAssayExperiment", "License", "Multiple experiments", "MultiAssayExperiment"], "titleterms": {"0": 4, "1": 4, "2": 4, "3": 4, "4": 4, "5": 4, "No": 8, "access": 8, "accessor": 8, "an": [5, 8], "anndata": 8, "case": 8, "chang": 5, "changelog": 4, "clone": 5, "code": 5, "column": 8, "complet": 8, "construct": 8, "content": [1, 2, 6], "contribut": 5, "contributor": 3, "creat": 5, "dimens": 8, "document": 5, "empti": 8, "environ": 5, "experi": 8, "function": 8, "getter": 8, "h5ad": 2, "helper": 8, "implement": 5, "improv": 5, "indic": [6, 8], "instal": [6, 9], "interfac": 2, "interop": 8, "intersect": 8, "io": 2, "issu": 5, "licens": 7, "mae": 8, "maintain": 5, "map": 8, "modul": [1, 2], "mudata": 8, "multiassayexperi": [0, 1, 2, 6, 9], "multipl": 8, "name": 8, "note": 9, "packag": [1, 2], "releas": 5, "replic": 8, "report": 5, "repositori": 5, "row": 8, "sampl": 8, "setter": 8, "submit": 5, "submodul": [1, 2], "subpackag": 1, "subset": 8, "tabl": 6, "task": 5, "todo": 5, "troubleshoot": 5, "usag": 9, "version": 4, "your": 5}}) \ No newline at end of file