From ce9e684be710f5f3ab3b804faaec0dcb9b750e62 Mon Sep 17 00:00:00 2001 From: LTLA Date: Sat, 11 Nov 2023 21:04:54 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20BiocPy/B?= =?UTF-8?q?iocFrame@cf752ccc5dee8e92c7e3c1f7b9c0170c06927b5d=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .buildinfo | 2 +- _modules/biocframe/BiocFrame.html | 2005 +++++++++++++----------- _modules/biocframe/Factor.html | 732 --------- _modules/biocframe/io/from_pandas.html | 20 +- _modules/index.html | 9 +- _sources/api/biocframe.rst.txt | 24 - _sources/index.md.txt | 11 - _static/documentation_options.js | 2 +- api/biocframe.html | 1306 +++++---------- api/biocframe.io.html | 19 +- api/modules.html | 66 +- authors.html | 8 +- changelog.html | 26 +- contributing.html | 8 +- genindex.html | 169 +- index.html | 34 +- license.html | 8 +- objects.inv | Bin 786 -> 695 bytes py-modindex.html | 26 +- readme.html | 406 +++-- search.html | 8 +- searchindex.js | 2 +- 22 files changed, 1888 insertions(+), 3003 deletions(-) delete mode 100644 _modules/biocframe/Factor.html diff --git a/.buildinfo b/.buildinfo index 6c63f7e..b5761ed 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: b53936228f1af9acd45a89c0634e3741 +config: d947c8425d53aaddc0e1df344d696ba8 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/_modules/biocframe/BiocFrame.html b/_modules/biocframe/BiocFrame.html index d18a8e2..cfcd2b0 100644 --- a/_modules/biocframe/BiocFrame.html +++ b/_modules/biocframe/BiocFrame.html @@ -5,7 +5,7 @@ - biocframe.BiocFrame - BiocFrame 0.4.1 documentation + biocframe.BiocFrame - BiocFrame 0.5.0 documentation @@ -122,7 +122,7 @@
-
BiocFrame 0.4.1 documentation
 +
BiocFrame 0.5.0 documentation
@@ -145,7 +145,7 @@
- BiocFrame 0.4.1 documentation + BiocFrame 0.5.0 documentation
@@ -1725,7 +1910,7 @@

Source code for biocframe.BiocFrame
-
+
diff --git a/_modules/biocframe/Factor.html b/_modules/biocframe/Factor.html deleted file mode 100644 index 6f7ca35..0000000 --- a/_modules/biocframe/Factor.html +++ /dev/null @@ -1,732 +0,0 @@ - - - - - - - - biocframe.Factor - BiocFrame 0.4.1 documentation - - - - - - - - - - - - - - - - Contents - - - - - - Menu - - - - - - - - Expand - - - - - - Light mode - - - - - - - - - - - - - - Dark mode - - - - - - - Auto light/dark mode - - - - - - - - - - - - - - - - - - - -
-
-
- -
-
-
BiocFrame 0.4.1 documentation
 -
-
-
- -
- -
-
- -
-
-
- - - - - Back to top - -
-
- -
- -
-
-

Source code for biocframe.Factor

-from copy import deepcopy
-from typing import List, Sequence, Union
-from warnings import warn
-
-import biocutils as ut
-from biocgenerics.combine import combine
-
-
-

-[docs]
-class Factor:
-    """Factor class, equivalent to R's ``factor``.
-
-    This is a vector of integer codes, each of which is an index into a list of unique strings. The aim is to encode a
-    list of strings as integers for easier numerical analysis.
-    """
-
-    def __init__(
-        self,
-        codes: Sequence[int],
-        levels: Sequence[str],
-        ordered: bool = False,
-        validate: bool = True,
-    ):
-        """Initialize a Factor object.
-
-        Args:
-            codes:
-                List of codes. Each value should be a non-negative
-                integer that is less than the length of ``levels``.
-                Entries may also be None.
-
-            levels:
-                List of levels containing unique strings.
-
-            ordered:
-                Whether the levels are ordered.
-
-            validate:
-                Whether to validate the arguments. Internal use only.
-        """
-        if not isinstance(codes, list):
-            codes = list(codes)
-        self._codes = codes  # could be more efficient with NumPy... but who cares.
-
-        if not isinstance(levels, list):
-            levels = list(levels)
-        self._levels = levels
-
-        self._ordered = ordered
-
-        if validate:
-            if not ut.is_list_of_type(self._codes, int, ignore_none=True):
-                raise TypeError("all entries of 'codes' should be integers or None")
-            if not ut.is_list_of_type(self._levels, str):
-                raise TypeError("all entries of 'levels' should be non-missing strings")
-
-            for x in codes:
-                if x is None:
-                    continue
-                if x < 0 or x >= len(self._levels):
-                    raise ValueError(
-                        "all entries of 'codes' should refer to an entry of 'levels'"
-                    )
-
-            if len(set(self._levels)) < len(self._levels):
-                raise ValueError("all entries of 'levels' should be unique")
-
-

-[docs]
-    def get_codes(self) -> List[int]:
-        """Get list of codes.
-
-        Returns:
-            List of codes, used as indices into the levels from
-            :py:attr:`~get_levels`. Values may also be None.
-        """
-        return self._codes

-
-
-    @property
-    def codes(self) -> List[int]:
-        """List of codes, used as indices into the levels from :py:attr:`~get_levels`. Values may also be None (read-
-        only property).
-
-        Returns:
-            List[int]: List of codes.
-        """
-        return self.get_codes()
-
-

-[docs]
-    def get_levels(self) -> List[str]:
-        """Get unique factor levels.
-
-        Returns:
-            List[str]: List of factor levels.
-        """
-        return self._levels

-
-
-    @property
-    def levels(self) -> List[str]:
-        """Get list of unique factor levels."""
-        return self.get_levels()
-
-    @levels.setter
-    def levels(self, levels: Union[str, List[str]]):
-        """Modify levels in the list (in-place operation).
-
-        Args:
-            levels (Union[str, List[str]]): A list of replacement levels. These should be unique strings
-                with no missing values.
-
-                Alternatively a single string containing an existing level in
-                this object. The new levels are defined as a permutation of the
-                existing levels where the provided string is now the first
-                level. The order of all other levels is preserved.
-        """
-        warn(
-            "Setting property 'levels'is an in-place operation, use 'set_levels' instead",
-            UserWarning,
-        )
-        self.set_levels(levels, in_place=True)
-
-

-[docs]
-    def get_ordered(self) -> bool:
-        """Get whether the levels are ordered.
-
-        Returns:
-            bool: True if ordered, otherwise False.
-        """
-        return self._ordered

-
-
-    @property
-    def ordered(self) -> bool:
-        """Get whether the levels are ordered (read-only).
-
-        Returns:
-            bool: True if ordered, otherwise False.
-        """
-        return self.get_ordered()
-
-

-[docs]
-    def __len__(self) -> int:
-        """Get length.
-
-        Returns:
-            Length of the factor in terms of the number of codes.
-        """
-        return len(self._codes)

-
-
-

-[docs]
-    def __repr__(self) -> str:
-        tmp = (
-            "Factor(codes="
-            + ut.print_truncated_list(self._codes)
-            + ", levels="
-            + ut.print_truncated_list(self._levels)
-        )
-        if self._ordered:
-            tmp += ", ordered=True"
-        tmp += ")"
-        return tmp

-
-
-    def __str__(self) -> str:
-        message = (
-            "Factor of length "
-            + str(len(self._codes))
-            + " with "
-            + str(len(self._levels))
-            + " level"
-        )
-        if len(self._levels) != 0:
-            message += "s"
-        message += "\n"
-
-        message += (
-            "values: "
-            + ut.print_truncated_list(self._codes, transform=lambda i: self._levels[i])
-            + "\n"
-        )
-        message += (
-            "levels: "
-            + ut.print_truncated_list(self._levels, transform=lambda x: x)
-            + "\n"
-        )
-        message += "ordered: " + str(self._ordered)
-        return message
-
-

-[docs]
-    def __getitem__(self, args: Union[int, Sequence[int]]) -> Union[str, "Factor"]:
-        """Subset the ``Factor`` list.
-
-        Args:
-            args:
-                Sequence of integers specifying the elements of interest.
-                Alternatively an integer specifying a single element.
-
-        Returns:
-            If ``args`` is a sequence, returns same type as caller (a new ``Factor``) containing
-            only the elements of interest from ``args``.
-
-            If ``args`` is an integer, a string is returned containing the
-            level corresponding to the code at position ``args``.
-        """
-        args, scalar = ut.normalize_subscript(args, len(self), None)
-        if scalar:
-            x = self._codes[args[0]]
-            if x is not None:
-                return self._levels[x]
-            else:
-                return x
-
-        new_codes = []
-        for i in args:
-            new_codes.append(self._codes[i])
-
-        current_class_const = type(self)
-        return current_class_const(
-            new_codes, self._levels, self._ordered, validate=False
-        )

-
-
-

-[docs]
-    def __setitem__(self, args: Sequence[int], value: "Factor"):
-        """Modify the ``Factor`` list.
-
-        Args:
-            args: Sequence of integers specifying the elements to be replaced.
-
-            value: A ``Factor`` containing the replacement values.
-
-        Returns:
-            The ``args`` elements in the current object are replaced with the
-            corresponding values in ``value``. This is performed by finding the
-            level for each entry of the replacement ``value``, matching it to a
-            level in the current object, and replacing the entry of ``codes``
-            with the code of the matched level. If there is no matching level,
-            None is inserted instead.
-        """
-        if isinstance(args, slice):
-            args = range(*args.indices(len(self._codes)))
-
-        if self._levels == value._levels:
-            for i, x in enumerate(args):
-                self._codes[x] = value._codes[i]
-        else:
-            lmapping = {}
-            for i, x in enumerate(self._levels):
-                lmapping[x] = i
-            mapping = []
-            for x in value._levels:
-                if x in lmapping:
-                    mapping.append(lmapping[x])
-                else:
-                    mapping.append(None)
-            for i, x in enumerate(args):
-                self._codes[x] = mapping[value._codes[i]]

-
-
-

-[docs]
-    def drop_unused_levels(self, in_place: bool = False) -> "Factor":
-        """Drop unused levels.
-
-        Args:
-            in_place: Whether to perform this modification in-place.
-
-        Returns:
-            If ``in_place = False``, returns same type as caller (a new ``Factor`` object)
-            where all unused levels have been removed.
-
-            If ``in_place = True``, unused levels are removed from the
-            current object; a reference to the current object is returned.
-        """
-        if in_place:
-            new_codes = self._codes
-        else:
-            new_codes = [None] * len(self._codes)
-
-        in_use = [False] * len(self._levels)
-        for x in self._codes:
-            if x is not None:
-                in_use[x] = True
-
-        new_levels = []
-        reindex = []
-        for i, x in enumerate(in_use):
-            if x:
-                reindex.append(len(new_levels))
-                new_levels.append(self._levels[i])
-            else:
-                reindex.append(None)
-
-        for i, x in enumerate(self._codes):
-            new_codes[i] = reindex[x]
-
-        if in_place:
-            self._levels = new_levels
-            return self
-        else:
-            current_class_const = type(self)
-            return current_class_const(
-                new_codes, new_levels, self._ordered, validate=False
-            )

-
-
-

-[docs]
-    def set_levels(
-        self, levels: Union[str, List[str]], in_place: bool = False
-    ) -> "Factor":
-        """Set or replace levels.
-
-        Args:
-            levels:
-                A list of replacement levels. These should be unique strings
-                with no missing values.
-
-                Alternatively a single string containing an existing level in
-                this object. The new levels are defined as a permutation of the
-                existing levels where the provided string is now the first
-                level. The order of all other levels is preserved.
-
-            in_place:
-                Whether to perform this modification in-place.
-
-        Returns:
-            If ``in_place = False``, returns same type as caller (a new ``Factor`` object) where
-            the levels have been replaced. This will automatically adjust the
-            codes so that they still refer to the same level in the new
-            ``levels``. If a code refers to a level that is not present in the
-            new ``levels``, it is replaced with None.
-
-            If ``in_place = True``, the levels are replaced in the current
-            object, and a reference to the current object is returned.
-        """
-        lmapping = {}
-        if isinstance(levels, str):
-            new_levels = [levels]
-            for x in self._levels:
-                if x == levels:
-                    lmapping[x] = 0
-                else:
-                    lmapping[x] = len(new_levels)
-                    new_levels.append(x)
-            if levels not in lmapping:
-                raise ValueError(
-                    "string 'levels' should already be present among object levels"
-                )
-        else:
-            if not ut.is_list_of_type(levels, str):
-                raise TypeError("all entries of 'levels' should be non-missing strings")
-            new_levels = levels
-            for i, x in enumerate(levels):
-                if x in lmapping:
-                    raise ValueError("levels should be unique")
-                lmapping[x] = i
-
-        mapping = [None] * len(self._levels)
-        for i, x in enumerate(self._levels):
-            if x in lmapping:
-                mapping[i] = lmapping[x]
-
-        new_codes = [None] * len(self._codes)
-        for i, x in enumerate(self._codes):
-            new_codes[i] = mapping[x]
-
-        if in_place:
-            self._codes = new_codes
-            self._levels = new_levels
-            return self
-        else:
-            current_class_const = type(self)
-            return current_class_const(
-                new_codes, new_levels, self._ordered, validate=False
-            )

-
-
-

-[docs]
-    def __copy__(self) -> "Factor":
-        """
-        Returns:
-            A shallow copy of the ``Factor`` object.
-        """
-        current_class_const = type(self)
-        return current_class_const(
-            self._codes, self._levels, self._ordered, validate=False
-        )

-
-
-

-[docs]
-    def __deepcopy__(self, memo) -> "Factor":
-        """
-        Returns:
-            A deep copy of the ``Factor`` object.
-        """
-        current_class_const = type(self)
-        return current_class_const(
-            deepcopy(self._codes, memo),
-            deepcopy(self._levels, memo),
-            self._ordered,
-            validate=False,
-        )

-
-
-

-[docs]
-    def to_pandas(self):
-        """Coerce to :py:class:`~pandas.Categorical` object.
-
-        Returns:
-            Categorical: A :py:class:`~pandas.Categorical` object.
-        """
-        from pandas import Categorical
-
-        return Categorical(
-            values=[self._levels[c] for c in self._codes],
-            ordered=self._ordered,
-        )

-
-
-

-[docs]
-    @staticmethod
-    def from_list(values: Sequence[str]) -> "Factor":
-        """Represent a categorical vector as a Factor.
-
-        Args:
-            values (Sequence[str]): List of strings
-
-        Raises:
-            ValueError: If values is not a list.
-
-        Returns:
-            Factor: A Factor object.
-        """
-        levels, indices = ut.factor(values)
-        return Factor(indices, levels=levels)

-

-
-
-
-@combine.register(Factor)
-def _combine_factors(*x: Factor):
-    if not ut.is_list_of_type(x, Factor):
-        raise ValueError("all elements to `combine` must be `Factor` objects")
-
-    first = x[0]
-    all_same = True
-    for f in x[1:]:
-        if f._levels != first._levels or f._ordered != first._ordered:
-            all_same = False
-            break
-
-    if all_same:
-        all_codes = []
-        for f in x:
-            all_codes.append(f._codes)
-        new_codes = combine(*all_codes)
-        new_levels = first._levels
-        new_ordered = first._ordered
-    else:
-        all_levels_map = {}
-        new_levels = []
-        new_codes = []
-        for f in x:
-            mapping = []
-            for i, y in enumerate(f._levels):
-                if y not in all_levels_map:
-                    all_levels_map[y] = len(new_levels)
-                    new_levels.append(y)
-                mapping.append(all_levels_map[y])
-            for j in f._codes:
-                if j is None:
-                    new_codes.append(None)
-                else:
-                    new_codes.append(mapping[j])
-        new_ordered = False
-
-    return Factor(new_codes, new_levels, new_ordered, validate=False)
-
-
-
-
- -
- - -
-
-
-
- Copyright © 2023, jkanche -
- Made with Sphinx and @pradyunsg's - - Furo - -
-
- -
-
- -
-
- -
-
- - - - - \ No newline at end of file diff --git a/_modules/biocframe/io/from_pandas.html b/_modules/biocframe/io/from_pandas.html index 2b8ed36..ebc90a4 100644 --- a/_modules/biocframe/io/from_pandas.html +++ b/_modules/biocframe/io/from_pandas.html @@ -5,7 +5,7 @@ - biocframe.io.from_pandas - BiocFrame 0.4.1 documentation + biocframe.io.from_pandas - BiocFrame 0.5.0 documentation @@ -122,7 +122,7 @@
-
BiocFrame 0.4.1 documentation
 +
BiocFrame 0.5.0 documentation
@@ -145,7 +145,7 @@
- BiocFrame 0.4.1 documentation + BiocFrame 0.5.0 documentation
-
BiocFrame 0.4.1 documentation
 +
BiocFrame 0.5.0 documentation
@@ -145,7 +145,7 @@
- BiocFrame 0.4.1 documentation + BiocFrame 0.5.0 documentation @@ -201,7 +201,6 @@ @@ -235,7 +234,7 @@

All modules for which code is available

-
+
diff --git a/_sources/api/biocframe.rst.txt b/_sources/api/biocframe.rst.txt index 73ed1fd..eef8159 100644 --- a/_sources/api/biocframe.rst.txt +++ b/_sources/api/biocframe.rst.txt @@ -20,30 +20,6 @@ biocframe.BiocFrame module :undoc-members: :show-inheritance: -biocframe.Factor module ------------------------ - -.. automodule:: biocframe.Factor - :members: - :undoc-members: - :show-inheritance: - -biocframe.types module ----------------------- - -.. automodule:: biocframe.types - :members: - :undoc-members: - :show-inheritance: - -biocframe.utils module ----------------------- - -.. automodule:: biocframe.utils - :members: - :undoc-members: - :show-inheritance: - Module contents --------------- diff --git a/_sources/index.md.txt b/_sources/index.md.txt index c725dae..e88d088 100644 --- a/_sources/index.md.txt +++ b/_sources/index.md.txt @@ -1,16 +1,5 @@ # BiocFrame -This package provides a data-frame representation similar to a pandas `DataFrame`, with -support for nested column types. - -## Install - -Package is published to [PyPI](https://pypi.org/project/biocframe/) - -```shell -pip install biocframe -``` - ## Contents ```{toctree} diff --git a/_static/documentation_options.js b/_static/documentation_options.js index 0145a7a..240446d 100644 --- a/_static/documentation_options.js +++ b/_static/documentation_options.js @@ -1,5 +1,5 @@ const DOCUMENTATION_OPTIONS = { - VERSION: '0.4.1', + VERSION: '0.5.0', LANGUAGE: 'en', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/api/biocframe.html b/api/biocframe.html index 8869f38..72fd896 100644 --- a/api/biocframe.html +++ b/api/biocframe.html @@ -6,7 +6,7 @@ - biocframe package - BiocFrame 0.4.1 documentation + biocframe package - BiocFrame 0.5.0 documentation @@ -123,7 +123,7 @@
-
BiocFrame 0.4.1 documentation
 +
BiocFrame 0.5.0 documentation
@@ -146,7 +146,7 @@
- BiocFrame 0.4.1 documentation + BiocFrame 0.5.0 documentation @@ -226,165 +226,31 @@

Submodules

biocframe.BiocFrame module#

-class biocframe.BiocFrame.BiocFrame(data=None, number_of_rows=None, row_names=None, column_names=None, mcols=None, metadata=None)[source]#
+class biocframe.BiocFrame.BiocFrame(data=None, number_of_rows=None, row_names=None, column_names=None, column_data=None, metadata=None, validate=True)[source]#

Bases: object

BiocFrame is an alternative to DataFrame, with support for nested and flexible column types. -Similar to R’s DataFrame class.

-

Columns are required to implement the length (__len__) and slice (__getitem__) dunder -methods. This allows BiocFrame to accept nested -BiocFrame or any supported class as columns.

-

Typical usage example:

-

To create a BiocFrame object, simply provide the data as a dictionary.

-
# made up ensembl ids.
-obj = {
-    "ensembl": ["ENS00001", "ENS00002", "ENS00003"],
-    "symbol": ["MAP1A", "BIN1", "ESR1"],
-}
-bframe = BiocFrame(obj)
-
-
-

Alternatively, you can specify BiocFrame class -as a column.

-
# made up chromosome locations and ensembl ids.
-obj = {
-    "ensembl": ["ENS00001", "ENS00002", "ENS00002"],
-    "symbol": ["MAP1A", "BIN1", "ESR1"],
-    "ranges": BiocFrame({
-        "chr": ["chr1", "chr2", "chr3"],
-        "start": [1000, 1100, 5000],
-        "end": [1100, 4000, 5500]
-    }),
-}
-bframe = BiocFrame(obj)
-
-
-

Methods are available to slice (__getitem__()) the object,

-
sliced = bframe[1:2, [True, False, False]]
-
-
-

Additionally, the slice operation accepts different inputs, you can either -specify a boolean vector, a slice object, or a list of indices or row names to subset.

-

To access a particular row or column of the dataframe,

-
row2 = bframe.row(2)
-ensembl_col = bframe.column("ensembl")
-
-
-

Use the combine() generic to concatenate multiple biocframe objects,

-
bframe1 = BiocFrame(
-    {
-        "odd": [1, 3, 5, 7, 9],
-        "even": [0, 2, 4, 6, 8],
-    }
-)
-
-bframe2 = BiocFrame(
-    {
-        "odd": [11, 33, 55, 77, 99],
-        "even": [0, 22, 44, 66, 88],
-    }
-)
-
-from biocgenerics.combine import combine
-combined = combine(bframe1, bframe2)
-
-
-

or the combine function

-
combined = bframe1.combine(bframe2)
-
-
-
-
-data#
-

Dictionary of column names as keys and -their values.

-
-
Type:
-

Dict[str, Any], optional

-
-
-
- -
-
-number_of_rows#
-

Number of rows.

-
-
Type:
-

int, optional

-
-
-
- -
-
-row_names#
-

Row names.

-
-
Type:
-

list, optional

-
-
-
- -
-
-column_names#
-

Column names.

-
-
Type:
-

list, optional

-
-
-
- -
-
-mcols#
-

Metadata about columns.

-
-
Type:
-

BiocFrame, optional

-
-
-
- -
-
-metadata#
-

Additional metadata.

-
-
Type:
-

dict

-
-
-
- -
-
Raises:
-

ValueError – If there is a mismatch in the number of rows or columns in the data.

-
-
+Inspired by the DFrame class from Bioconductor’s S4Vectors package. Any object may be used as a column, +provided it has:

+
    +

  • Some concept of “height”, as defined by get_height() from BiocUtils. +This defaults to the length as defined by __len__.

    • +

  • The ability to be sliced by integer indices, as implemented by subset() from BiocUtils. +This defaults to calling __getitem__.

    • +

  • The ability to be combined with other objects, as implemented in combine() from BiocUtils.

    • +

  • The ability to perform an assignment, as implemented in assign() from BiocUtils.

    • +
+

This allows BiocFrame to accept arbitrarily complex classes (such as nested BiocFrame instances) as columns.

__array_ufunc__(func, method, *inputs, **kwargs)[source]#
-

Interface with NumPy array methods.

+

Interface for NumPy array methods.

Note: This is a very primitive implementation and needs tests to support different types.

-

Usage:

-
np.sqrt(biocframe)
-
-
-
Raises:
-
-
-
Return type:
-

BiocFrame

+
Return type:
+

BiocFrame

-
Returns:
-

An object with the same type as the caller.

+
Returns:
+

An object with the same type as the caller.

@@ -392,11 +258,9 @@

Submodules
__copy__()[source]#
-

Make a shallow copy of the object.

-

Any modifications to the copied object may also affect the original.

-
+
Returns:
-

The same type as caller.

+

A shallow copy of the current BiocFrame.

@@ -404,13 +268,9 @@

Submodules
__deepcopy__(memo=None, _nil=[])[source]#
-

Make a deep copy of the object.

-
-
Raises:
-

Exception – If a column cannot be copied.

-
-
Returns:
-

The same type as caller.

+
+
Returns:
+

A deep copy of the current BiocFrame.

@@ -418,112 +278,68 @@

Submodules
__delitem__(name)[source]#
-

Remove a column (in-place operation).

-

Usage:

-
# made-up chromosome locations and ensembl ids.
-obj = {
-    "ensembl": ["ENS00001", "ENS00002", "ENS00002"],
-    "symbol": ["MAP1A", "BIN1", "ESR1"],
-    "ranges": BiocFrame({
-        "chr": ["chr1", "chr2", "chr3"],
-        "start": [1000, 1100, 5000],
-        "end": [1100, 4000, 5500]
-    }),
-}
-bframe = BiocFrame(obj)
-delete bframe["symbol"]
-
-
-
-
Parameters:
-

name (str) – Name of the column.

-
-
Raises:
-

ValueError – If name is not a valid column.

-
-
+

Alias for remove_column with in_place = True.

+

As this mutates the original object, a warning is raised.

__getitem__(args)[source]#
-

Subset the data frame.

-

This operation returns a new object with the same type as the caller. -If you need to access specific rows or columns, use the -row() or -column() -methods.

-

Usage:

-
# made up chromosome locations and ensembl ids.
-obj = {
-    "ensembl": ["ENS00001", "ENS00002", "ENS00002"],
-    "symbol": ["MAP1A", "BIN1", "ESR1"],
-    "ranges": BiocFrame({
-        "chr": ["chr1", "chr2", "chr3"],
-        "start": [1000, 1100, 5000],
-        "end": [1100, 4000, 5500]
-    }),
-}
-bframe = BiocFrame(obj)
-
-# Different ways to slice.
-
-bframe[0:2, 0:2]
-bframe[[0, 2], [True, False, False]]
-bframe[<List of column names>]
-
-
+

Wrapper around get_column and get_slice to obtain a slice of a BiocFrame or any +of its columns.

Parameters:
-

args (SlicerArgTypes) –

A Tuple of slicer arguments to subset rows and -columns. An element in args may be,

-
    -
  • -
    List of booleans, True to keep the row/column, False to remove.

    The length of the boolean vector must be the same as the number of rows/columns.

    -
    -
    -
    • -

  • List of integer positions along rows/columns to keep.

    • -

  • A slice object specifying the list of indices to keep.

    • -
  • -
    A list of index names to keep. For rows, the object must contain unique

    row_names, and for columns must -contain unique column_names.

    -
    -
    -
    • -
  • -
    An integer to subset either a single row or column index.

    Alternatively, you might want to use -row() or -column() methods.

    -
    -
    -
    • -
  • -
    A string to subset either a single row or column by label.

    Alternatively, you might want to use -row() or -column() methods.

    -
    -
    -
    • -
+

args (Union[int, str, Sequence, tuple]) –

A sequence or a scalar integer or string, specifying the +columns to retain based on their names or indices.

+

Alternatively a tuple of length 1. The first entry specifies +the rows to retain based on their names or indices.

+

Alternatively a tuple of length 2. The first entry specifies +the rows to retain, while the second entry specifies the +columns to retain, based on their names or indices.

-
Raises:
-
    -

  • ValueError – If too many slices are provided.

    • -

  • TypeError – If the provided args are not of the expected type.

    • -
+
Return type:
+

Union[BiocFrame, Any]

Returns:
-

    -

  • If a single row is sliced, returns a dict.

    • -

  • If a single column is sliced, returns returns the same type of the column.

    • -

  • For all other scenarios, returns the same type as the caller with the subsetted rows and columns.

    • -
+

If args is a scalar, the specified column is returned. This is +achieved internally by calling get_column.

+

If args is a sequence, a new BiocFrame is returned +containing only the specified columns. This is achieved by just +calling get_slice with no row slicing.

+

If args is a tuple of length 1, a new BiocFrame is returned +containing the specified rows. This is achieved by just calling +get_slice with no column slicing.

+

If args is a tuple of length 2, a new BiocFrame is returned +containing the specified rows and columns. This is achieved by just +calling get_slice with the specified arguments.

-
Return type:
-

Union[“BiocFrame”, dict, list]

+
+
+ +
+
+__init__(data=None, number_of_rows=None, row_names=None, column_names=None, column_data=None, metadata=None, validate=True)[source]#
+

Initialize a BiocFrame object from columns.

+
+
Parameters:
+
    +

  • data (Optional[Dict[str, Any]]) – Dictionary of column names as keys and their values. All +columns must have the same length. Defaults to an empty +dictionary.

    • +

  • number_of_rows (Optional[int]) – Number of rows. If not specified, inferred from data. This +needs to be provided if data is empty and row_names are +not present.

    • +

  • row_names (Optional[List]) – Row names. This should not contain missing strings.

    • +

  • column_names (Optional[List[str]]) – Column names. If not provided, inferred from the data. +This may be in a different order than the keys of data. +This should not contain missing strings.

    • +

  • column_data (Optional[BiocFrame]) – Metadata about columns. Must have the same number of rows as +the length of column_names. Defaults to None.

    • +

  • metadata (Optional[dict]) – Additional metadata. Defaults to an empty dictionary.

    • +

  • validate (bool) – Internal use only.

    • +
@@ -534,7 +350,7 @@

Submodules
Return type:
-

BiocFrameIter

+

BiocFrameIter

@@ -542,13 +358,12 @@

Submodules
__len__()[source]#
-

Number of rows.

-
-
Returns:
-

Number of rows.

+
+
Return type:
+

int

-
Return type:
-

int

+
Returns:
+

Number of rows.

@@ -556,10 +371,12 @@

Submodules
__repr__()[source]#
-

Return repr(self).

-
+
Return type:
-

str

+

str

+
+
Returns:
+

A string representation of this BiocFrame.

@@ -567,186 +384,104 @@

Submodules
__setitem__(args, value)[source]#
-

Add or re-assign a value to a column (in-place operation).

-

Usage:

-
# Made-up chromosome locations and ensembl ids.
-obj = {
-    "ensembl": ["ENS00001", "ENS00002", "ENS00002"],
-    "symbol": ["MAP1A", "BIN1", "ESR1"],
-    "ranges": BiocFrame({
-        "chr": ["chr1", "chr2", "chr3"],
-        "start": [1000, 1100, 5000],
-        "end": [1100, 4000, 5500]
-    }),
-}
-bframe = BiocFrame(obj)
-
-bframe["symbol"] = ["gene_a", "gene_b", "gene_c"]
-
-
-
-
Parameters:
-
    -

  • args (str) – Name of the column.

    • -

  • value (List) – New value to set.

    • -
-
-
Raises:
-

ValueError – If the length of value does not match the number of rows.

-
-
+

Wrapper around set_column and set_slice to modify a slice of a BiocFrame or any +of its columns. As this modified the original object in place, a warning is raise.

+

If args is a string, it is assumed to be a column name and +value is expected to be the column contents; these are passed onto +set_column with in_place = True.

+

If args is a tuple, it is assumed to contain row and column indices. +value is expected to be a BiocFrame containing replacement values. +These are passed to set_slice with in_place = True.

-property colnames: list#
-

Alias to column_names().

-
-
Returns:
-

list of column names.

-
-
Return type:
-

list

-
-
+property colnames: StringList# +

Alias for get_column_names, provided for back-compatibility only.

-column(index_or_name)[source]#
-

Access a column by index or column label. Alias to get_column().

+column(column)[source]# +

Alias for get_column(), provided for back-compatibility only.

-
Parameters:
-

index_or_name (Union[str, int]) –

Name of the column, which must a valid name in -column_names.

-

Alternatively, you may provide the integer index of the column to access.

-

-
-
Raises:
-
    -

  • ValueError – If index_or_name is not in column names. - If the integer index is greater than the number of columns.

    • -

  • TypeError – If index_or_name is neither a string nor an integer.

    • -
-
-
Returns:
-

Column with its original type preserved.

-
-
Return type:
-

Any

+
Return type:
+

Any

-
-property column_names: List[str]#
-

Column names of the BiocFrame.

-
-
Returns:
-

A list of column names.

-
-
Return type:
-

List[str]

-
-
+
+property column_data: None | BiocFrame#
+

Alias for get_column_data.

+
+ +
+
+property column_names: StringList#
+

Alias for get_column_names.

-property columns: list#
-

Alias to column_names().

-
-
Returns:
-

List of column names.

-
-
Return type:
-

list

-
-
+property columns: StringList# +

Alias for get_column_names, provided for compatibility with pandas.

combine(*other)[source]#
-

Combine multiple BiocFrame objects by row.

-

Note: Fills missing columns with an array of `None`s.

-
-
Parameters:
-

*other (BiocFrame) – BiocFrame objects.

-
-
Raises:
-

TypeError – If all objects are not of type BiocFrame.

-
-
Returns:
-

The same type as caller with the combined data.

-
-
+

Wrapper around relaxed_combine_rows(), provided for back-compatibility only.

copy()[source]#
-

Alias to __copy__().

-
-
Returns:
-

The same type as caller.

-
-
+

Alias for __copy__().

-
-property data: Dict[str, Any]#
-

Access columns as dict Read-only property.

-
-
Returns:
-

Dictionary of columns and their values.

-
-
Return type:
-

Dict[str, Any]

-
-
+
+property data: Dict[str, Any]#
+

Alias for get_data.

property dims: Tuple[int, int]#
-

Alias to shape().

-
-
Returns:
-

A tuple (m, n), -where m is the number of rows, and n is the number of columns.

-
-
Return type:
-

Tuple[int, int]

-
-
+

Alias for shape.

-get_column(index_or_name)[source]#
-

Access a column by index or column label.

-
+get_column(column)[source]# +
Parameters:
-

index_or_name (Union[str, int]) –

Name of the column, which must a valid name in -column_names.

-

Alternatively, you may provide the integer index of the column to access.

+

column (Union[str, int]) –

Name of the column, which must exist in get_column_names.

+

Alternatively, the integer index of the column of interest.

-
Raises:
-
    -

  • ValueError – If index_or_name is not in column names. - If the integer index is greater than the number of columns.

    • -

  • TypeError – If index_or_name is neither a string nor an integer.

    • -
+
Return type:
+

Any

Returns:
-

Column with its original type preserved.

+

The contents of the specified column.

-
Return type:
-

Any

+
+
+ +
+
+get_column_data()[source]#
+
+
Return type:
+

Optional[BiocFrame]

+
+
Returns:
+

The annotations for each column. This may be None if no annotation +is present, or is a BiocFrame where each row corresponds to a +column and contains that column’s metadata.

@@ -754,24 +489,25 @@

Submodules
get_column_names()[source]#
-

Column names of the BiocFrame.

-
-
Returns:
-

A list of column names.

+
+
Return type:
+

StringList

-
Return type:
-

List[str]

+
Returns:
+

A list of column names.

-
-get_mcols()[source]#
-

The mcols, containing annotation on the columns.

-
+
+get_data()[source]#
+
Return type:
-

Optional[BiocFrame]

+

Dict[str, Any]

+
+
Returns:
+

Dictionary of columns and their values.

@@ -779,40 +515,33 @@

Submodules
get_metadata()[source]#
-

Access metadata.

-
-
Returns:
-

Metadata object.

+
+
Return type:
+

dict

-
Return type:
-

dict

+
Returns:
+

Dictionary of metadata for this object.

-get_row(index_or_name)[source]#
-

Access a row by index or row name.Alias to get_row().

-
+get_row(row)[source]# +
Parameters:
-

index_or_name (Union[str, int]) –

Integer index of the row to access.

-

Alternatively, you may provide a string specifying the row to access, -only if row_names are available.

+

row (Union[str, int]) –

Integer index of the row to access.

+

If row names are available (see get_row_names), a +string may be supplied instead. The first occurrence of the +string in the row names is used.

-
Raises:
-
    -

  • ValueError – If index_or_name is not in row names. - If the integer index is greater than the number of rows.

    • -

  • TypeError – If index_or_name is neither a string nor an integer.

    • -
+
Return type:
+

dict

Returns:
-

A dictionary with keys as column names and their values.

-
-
Return type:
-

dict

+

A dictionary where the keys are column names and the values are +the contents of the columns at the specified row.

@@ -820,217 +549,225 @@

Submodules
get_row_names()[source]#
-

Row names of the BiocFrame.

-
-
Returns:
-

Row names if available, otherwise None.

+
+
Return type:
+

Optional[StringList]

-
Return type:
-

(List, optional)

+
Returns:
+

List of row names, or None if no row names are available.

-
-has_column(name)[source]#
-

Check whether the column exists in the BiocFrame.

+
+get_slice(rows, columns)[source]#
+

Slice BiocFrame along the rows and/or columns, based on their indices or names.

Parameters:
-

name (str) – Name to check.

+
    +

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

    Rows to be extracted. This may be an integer, boolean, string, +or any sequence thereof, as supported by +normalize_subscript(). +Scalars are treated as length-1 sequences.

    +

    Strings may only be used if row names are available (see +get_row_names). The first occurrence of each string +in the row names is used for extraction.

    +

    • +

  • columns (Union[str, int, bool, Sequence]) – Columns to be extracted. This may be an integer, boolean, +string, or any sequence thereof, as supported by +normalize_subscript(). +Scalars are treated as length-1 sequences.

    • +
-
Returns:
-

True if the column exists, otherwise False.

+
Return type:
+

BiocFrame

-
Return type:
-

bool

+
Returns:
+

A BiocFrame with the specified rows and columns.

-
-
-property index: list | None#
-

Alias to row_names().

-
-
Returns:
-

List of row names if available, otherwise None.

+
+
+has_column(name)[source]#
+
+
Parameters:
+

name (str) – Name of the column.

Return type:
-

(list, optional)

+

bool

+
+
Returns:
+

Whether a column with the specified name exists in this object.

-
-property mcols: None | BiocFrame#
-

The mcols, containing annotation on the columns.

+
+property index: StringList | None#
+

Alias to get_row_names, provided for compatibility with pandas.

-
-property metadata: dict#
-

Access metadata.

-
-
Returns:
-

Metadata object.

-
-
Return type:
-

dict

-
-
+
+property metadata: dict#
+

Alias for get_metadata.

-remove_column(name, in_place=False)[source]#
-

Remove a column.

+remove_column(column, in_place=False)[source]# +

Remove a column. This is a convenience wrapper around remove_columns.

Parameters:
    -

  • name (str) – Name of the column to remove.

    • -

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

    • +

  • column (Union[int, str]) – Name or positional index of the column to remove.

    • +

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

-
Raises:
-

ValueError – If column does not exist.

+
Return type:
+

BiocFrame

Returns:

A modified BiocFrame object, either as a copy of the original or as a reference to the (in-place-modified) original.

-
Return type:
-

BiocFrame

-
-
-row(index_or_name)[source]#
-

Access a row by index or row name.

+
+remove_columns(columns, in_place=False)[source]#
+

Remove any number of existing columns.

Parameters:
-

index_or_name (Union[str, int]) –

Integer index of the row to access.

-

Alternatively, you may provide a string specifying the row to access, -only if row_names are available.

-

-
-
Raises:
-
    -

  • ValueError – If index_or_name is not in row names. - If the integer index is greater than the number of rows.

    • -

  • TypeError – If index_or_name is neither a string nor an integer.

    • +
      +

    • columns (Sequence[Union[int, str]]) – Names or indices of the columns to remove.

      • +

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

    -
    Returns:
    -

    A dictionary with keys as column names and their values.

    +
    Returns:
    +

    A modified BiocFrame object, either as a copy of the original +or as a reference to the (in-place-modified) original.

    -
    Return type:
    -

    dict

    +
    Return type:
    +

    BiocFrame

-
-
-property row_names: List | None#
-

Row names of the BiocFrame.

+
+
+row(row)[source]#
+

Alias for get_row, provided for back-compatibility only.

-
Returns:
-

Row names if available, otherwise None.

-
-
Return type:
-

(List, optional)

+
Return type:
+

dict

+
+
+property row_names: StringList | None#
+

Alias for get_row_names.

+
+
-property rownames: list | None#
-

Alias to row_names().

+property rownames: StringList | None# +

Alias for get_row_names, provided for back-compatibility.

+
+ +
+
+set_column(column, value, in_place=False)[source]#
+

Modify an existing column or add a new column. This is a convenience wrapper around set_columns.

-
Returns:
-

List of row names if available, otherwise None.

+
Parameters:
+
    +

  • column (Union[int, str]) – Name of an existing or new column. Alternatively, an index +specifying the position of an existing column.

    • +

  • value (Any) – Value of the new column. This should have the same height +as the number of rows in the current object.

    • +

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

    • +
Return type:
-

(list, optional)

+

BiocFrame

+
+
Returns:
+

A modified BiocFrame object, either as a copy of the original +or as a reference to the (in-place-modified) original.

-
-set_column(args, value, in_place=False)[source]#
-

Set or Modify a column.

-
+
+set_column_data(column_data, in_place=False)[source]#
+
Parameters:
    -

  • args (SlicerArgTypes) – Name of the column.

    • -

  • value (Union[List, "BiocFrame"]) – New value to set.

    • -

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

    • +

  • column_data (Optional[BiocFrame]) – New column data. This should either be a BiocFrame with the +numbero of rows equal to the number of columns in the current object, +or None to remove existing column data.

    • +

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

-
Raises:
-
    -

  • TypeError – If row indices are not a sequence or slice.

    • -

  • ValueError – If length of value does not match the number of rows.

    • -
+
Return type:
+

BiocFrame

Returns:

A modified BiocFrame object, either as a copy of the original or as a reference to the (in-place-modified) original.

-
Return type:
-

BiocFrame

-
set_column_names(names, in_place=False)[source]#
-

Set new column names. New names must be unique.

-
+
Parameters:
    -

  • names (List[str]) – A list of unique values.

    • -

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

    • +

  • names (List[str]) – List of unique strings, of length equal to the number of +columns in this BiocFrame.

    • +

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

-
Raises:
-

ValueError – If the length of names does not match the number of columns. - If names is not unique.

+
Return type:
+

BiocFrame

Returns:

A modified BiocFrame object, either as a copy of the original or as a reference to the (in-place-modified) original.

-
Return type:
-

BiocFrame

-
-
-set_mcols(mcols, in_place=False)[source]#
-

Set new mcols, containing annotations on the columns.

+
+set_columns(columns, in_place=False)[source]#
+

Modify existing columns or add new columns.

Parameters:
    -

  • mcols (Biocframe, optional) – New mcols. Can be None to remove this information.

    • -

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

    • +

  • columns (Dict[str, Any]) – Contents of the columns to set. Keys may be strings containing +new or existing column names, or integers containing the position +of the column. Values should be the contents of each column.

    • +

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

-
Returns:
-

A modified BiocFrame object, either as a copy of the original -or as a reference to the (in-place-modified) original.

+
Return type:
+

BiocFrame

-
Return type:
-

BiocFrame

+
Returns:
+

A modified BiocFrame object, either as a copy of the original +or as a reference to the (in-place-modified) original.

@@ -1038,20 +775,19 @@

Submodules
set_metadata(metadata, in_place=False)[source]#
-

Set new metadata.

-
+
Parameters:
    -

  • metadata (dict) – New metadata object.

    • -

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

    • +

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

    • +

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

-
Returns:
-

A modified BiocFrame object, either as a copy of the original -or as a reference to the (in-place-modified) original.

+
Return type:
+

BiocFrame

-
Return type:
-

BiocFrame

+
Returns:
+

A modified BiocFrame object, either as a copy of the original +or as a reference to the (in-place-modified) original.

@@ -1059,71 +795,74 @@

Submodules
set_row_names(names, in_place=False)[source]#
-

Set new row names. All values in names must be unique.

-
+
Parameters:
    -

  • names (List[str], optional) – A list of unique values.

    • -

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

    • +

  • names (Optional[List]) – List of strings. This should have length equal to the +number of rows in the current BiocFrame.

    • +

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

-
Raises:
-
    -

  • ValueError – If the length of names does not match the number of rows.

    • -

  • ValueError – If names is not unique.

    • -
+
Return type:
+

BiocFrame

Returns:

A modified BiocFrame object, either as a copy of the original or as a reference to the (in-place-modified) original.

-
Return type:
-

BiocFrame

-
-
-
-property shape: Tuple[int, int]#
-

Dimensionality of the BiocFrame.

+
+
+set_slice(rows, columns, value, in_place=True)[source]#
+

Replace a slice of the BiocFrame given the row and columns of the slice.

-
Returns:
-

A tuple (m, n), -where m is the number of rows, and n is the number of columns.

+
Parameters:
+
    +

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

    Rows to be replaced. This may be any sequence of strings, +integers, or booleans (or mixture thereof), as supported by +normalize_subscript(). +Scalars are treated as length-1 sequences.

    +

    Strings may only be used if row names are available (see +get_row_names). The first occurrence of each string +in the row names is used for extraction.

    +

    • +

  • columns (Union[int, str, bool, Sequence]) – Columns to be replaced. This may be any sequence of strings, +integers, or booleans (or mixture thereof), as supported by +normalize_subscript(). +Scalars are treated as length-1 sequences.

    • +

  • value (BiocFrame) – A BiocFrame containing replacement values. Each row +corresponds to a row in rows, while each column corresponds +to a column in columns. Note that the replacement is based +on position, so row and column names in value are ignored.

    • +

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

    • +
Return type:
-

Tuple[int, int]

+

BiocFrame

+
+
Returns:
+

A modified BiocFrame object, either as a copy of the original +or as a reference to the (in-place-modified) original.

+
+
+property shape: Tuple[int, int]#
+

Returns: +Tuple containing the number of rows and columns in this BiocFrame.

+
+
-slice(row_indices_or_names=None, column_indices_or_names=None)[source]#
-

Slice BiocFrame by index or values.

+slice(rows, columns)[source]# +

Alias for __getitem__, for back-compatibility.

-
Parameters:
-
    -

  • row_indices_or_names (SlicerTypes, optional) –

    Row indices (index positions) -or row names (string) to slice.

    -

    Object must contain biocframe.BiocFrame.BiocFrame.row_names to slice by names. -Defaults to None.

    -

    • -

  • column_indices_or_names (SlicerTypes, optional) – Column indices (index positions) -or column names (string) to slice. Defaults to None.

    • -
-
-
Returns:
-

    -

  • If a single row is sliced, returns a dict.

    • -

  • If a single column is sliced, returns the same type of the column.

    • -

  • For all other scenarios, returns the same type as the caller with the subsetted rows and columns.

    • -
-

-
Return type:
-

Union[“BiocFrame”, dict, list]

+

BiocFrame

@@ -1131,13 +870,13 @@

Submodules
to_pandas()[source]#
-

Convert BiocFrame into DataFrame object.

+

Convert the BiocFrame into a DataFrame object.

-
Returns:
-

A DataFrame object.

+
Return type:
+

pandas.DataFrame

-
Return type:
-

DataFrame

+
Returns:
+

A DataFrame object.

@@ -1155,296 +894,101 @@

Submodules -
-__iter__()[source]#
-

- -
-
-__next__()[source]#
-
- -
- - -
-

biocframe.Factor module#

-
-
-class biocframe.Factor.Factor(codes, levels, ordered=False, validate=True)[source]#
-

Bases: object

-

Factor class, equivalent to R’s factor.

-

This is a vector of integer codes, each of which is an index into a list of unique strings. The aim is to encode a -list of strings as integers for easier numerical analysis.

-
-
-__copy__()[source]#
-
-
Return type:
-

Factor

-
-
Returns:
-

A shallow copy of the Factor object.

-
-
-
- -
-
-__deepcopy__(memo)[source]#
-
-
Return type:
-

Factor

-
-
Returns:
-

A deep copy of the Factor object.

-
-
-
- -
-
-__getitem__(args)[source]#
-

Subset the Factor list.

+
+__init__(obj)[source]#
+

Initialize the iterator.

Parameters:
-

args (Union[int, Sequence[int]]) – Sequence of integers specifying the elements of interest. -Alternatively an integer specifying a single element.

-
-
Return type:
-

Union[str, Factor]

-
-
Returns:
-

If args is a sequence, returns same type as caller (a new Factor) containing -only the elements of interest from args.

-

If args is an integer, a string is returned containing the -level corresponding to the code at position args.

-

+

obj (BiocFrame) – source object to iterate.

-
-__len__()[source]#
-

Get length.

-
-
Return type:
-

int

-
-
Returns:
-

Length of the factor in terms of the number of codes.

-
-
-
+
+__iter__()[source]#
+
-
-__repr__()[source]#
-

Return repr(self).

-
-
Return type:
-

str

-
-
+
+__next__()[source]#
+
+
-
-
-__setitem__(args, value)[source]#
-

Modify the Factor list.

+
+
+biocframe.BiocFrame.merge(x, by=None, join='left', rename_duplicate_columns=False)[source]#
+

Merge multiple BiocFrame` objects together by common columns or row names, yielding a combined +object with a union of columns across all objects.

Parameters:
    -

  • args (Sequence[int]) – Sequence of integers specifying the elements to be replaced.

    • -

  • value (Factor) – A Factor containing the replacement values.

    • +

  • x (Sequence[BiocFrame]) – Sequence of BiocFrame objects. Each object may have any +number and identity of rows and columns.

    • +

  • by (Union[None, str, Sequence]) –

    If string, the name of column containing the keys. Each entry of +x is assumed to have this column.

    +

    If integer, the index of column containing the keys. The same +index is used for each entry of x.

    +

    If None, keys are assumed to be present in the row names.

    +

    Alternatively a sequence of strings, integers or None, specifying +the location of the keys in each entry of x.

    +

    • +

  • join (Literal['inner', 'left', 'right', 'outer']) – Strategy for the merge. For left and right joins, we consider the +keys for the first and last object in x, respectively.

    • +

  • rename_duplicate_columns (bool) – Whether duplicated non-key columns across x should be +automatically renamed in the merged object. If False, an error is +raised instead.

Returns:
-

The args elements in the current object are replaced with the -corresponding values in value. This is performed by finding the -level for each entry of the replacement value, matching it to a -level in the current object, and replacing the entry of codes -with the code of the matched level. If there is no matching level, -None is inserted instead.

-
-
-
- -
-
-property codes: List[int]#
-

List of codes, used as indices into the levels from get_levels. Values may also be None (read- -only property).

-
-
Returns:
-

List of codes.

-
-
Return type:
-

List[int]

-
-
-
- -
-
-drop_unused_levels(in_place=False)[source]#
-

Drop unused levels.

-
-
Parameters:
-

in_place (bool) – Whether to perform this modification in-place.

-
-
Return type:
-

Factor

-
-
Returns:
-

If in_place = False, returns same type as caller (a new Factor object) -where all unused levels have been removed.

-

If in_place = True, unused levels are removed from the -current object; a reference to the current object is returned.

+

A BiocFrame containing the merged contents.

+

If by = None, the keys are stored in the row names.

+

If by is a string, keys are stored in the column of the same name.

+

If by is a sequence, keys are stored in the row names if by[0] = +None, otherwise they are stored in the column named by[0].

-
-
- -
-
-static from_list(values)[source]#
-

Represent a categorical vector as a Factor.

-
-
Parameters:
-

values (Sequence[str]) – List of strings

-
-
Raises:
-

ValueError – If values is not a list.

-
-
Returns:
-

A Factor object.

-
-
Return type:
-

Factor

-
-
-
- -
-
-get_codes()[source]#
-

Get list of codes.

-
Return type:
-

List[int]

-
-
Returns:
-

List of codes, used as indices into the levels from -get_levels. Values may also be None.

-
-
-
- -
-
-get_levels()[source]#
-

Get unique factor levels.

-
-
Returns:
-

List of factor levels.

-
-
Return type:
-

List[str]

+

BiocFrame

-
-
-get_ordered()[source]#
-

Get whether the levels are ordered.

+
+
+biocframe.BiocFrame.relaxed_combine_columns(*x)[source]#
+

Wrapper around merge() that performs a left join on the row names.

-
Returns:
-

True if ordered, otherwise False.

-
-
Return type:
-

bool

+
Return type:
+

BiocFrame

-
-
-property levels: List[str]#
-

Get list of unique factor levels.

-
- -
-
-property ordered: bool#
-

Get whether the levels are ordered (read-only).

-
-
Returns:
-

True if ordered, otherwise False.

-
-
Return type:
-

bool

-
-
-
- -
-
-set_levels(levels, in_place=False)[source]#
-

Set or replace levels.

+
+
+biocframe.BiocFrame.relaxed_combine_rows(*x)[source]#
+

A relaxed version of the combine_rows() method for BiocFrame +objects. Whereas combine_rows expects that all objects have the same columns, relaxed_combine_rows allows +for different columns. Absent columns in any object are filled in with appropriate placeholder values before +combining.

Parameters:
-
    -

  • levels (Union[str, List[str]]) –

    A list of replacement levels. These should be unique strings -with no missing values.

    -

    Alternatively a single string containing an existing level in -this object. The new levels are defined as a permutation of the -existing levels where the provided string is now the first -level. The order of all other levels is preserved.

    -

    • -

  • in_place (bool) – Whether to perform this modification in-place.

    • -
+

x (BiocFrame) – One or more BiocFrame objects, possibly with differences in the +number and identity of their columns.

Return type:
-

Factor

+

BiocFrame

Returns:
-

If in_place = False, returns same type as caller (a new Factor object) where -the levels have been replaced. This will automatically adjust the -codes so that they still refer to the same level in the new -levels. If a code refers to a level that is not present in the -new levels, it is replaced with None.

-

If in_place = True, the levels are replaced in the current -object, and a reference to the current object is returned.

-

+

A BiocFrame that combines all x along their rows and contains +the union of all columns. Columns absent in any x are filled in +with placeholders consisting of Nones or masked NumPy values.

-
-
-to_pandas()[source]#
-

Coerce to Categorical object.

-
-
Returns:
-

A Categorical object.

-
-
Return type:
-

Categorical

-
-
-
- -
- - -
-

biocframe.types module#

-
-
-

biocframe.utils module#

Module contents#

@@ -1511,84 +1055,64 @@

SubmodulesSubmodules
  • biocframe.BiocFrame module
    • -
  • biocframe.Factor module -
    • -
  • biocframe.types module
    • -
  • biocframe.utils module
  • Module contents
    • @@ -1601,7 +1125,7 @@

    Submodules +

    diff --git a/api/biocframe.io.html b/api/biocframe.io.html index fb93032..0fac53d 100644 --- a/api/biocframe.io.html +++ b/api/biocframe.io.html @@ -6,7 +6,7 @@ - biocframe.io package - BiocFrame 0.4.1 documentation + biocframe.io package - BiocFrame 0.5.0 documentation @@ -123,7 +123,7 @@
    -
    BiocFrame 0.4.1 documentation
     +
    BiocFrame 0.5.0 documentation
    @@ -146,7 +146,7 @@
    - BiocFrame 0.4.1 documentation + BiocFrame 0.5.0 documentation @@ -211,20 +211,17 @@

    Submodules
    biocframe.io.from_pandas.from_pandas(input)[source]#
    -

    Read a BiocFrame from a DataFrame object.

    +

    Create a BiocFrame from a DataFrame object.

    Parameters:
    -

    input (DataFrame) – Input data.

    +

    input (pandas.DataFrame) – Input data.

    -
    Raises:
    -

    TypeError – If input is not a DataFrame.

    +
    Return type:
    +

    BiocFrame

    Returns:

    A BiocFrame object.

    -
    Return type:
    -

    BiocFrame

    -
    @@ -307,7 +304,7 @@

    Submodules +

    diff --git a/api/modules.html b/api/modules.html index 32b0c9c..1619f02 100644 --- a/api/modules.html +++ b/api/modules.html @@ -3,10 +3,10 @@ - + - biocframe - BiocFrame 0.4.1 documentation + biocframe - BiocFrame 0.5.0 documentation @@ -123,7 +123,7 @@
    -
    BiocFrame 0.4.1 documentation
     +
    BiocFrame 0.5.0 documentation
    @@ -146,7 +146,7 @@
    - BiocFrame 0.4.1 documentation + BiocFrame 0.5.0 documentation @@ -218,84 +218,64 @@

    biocframeSubmodules
  • biocframe.BiocFrame module
    • -
  • biocframe.Factor module -
    • -
  • biocframe.types module
    • -
  • biocframe.utils module
  • Module contents
    • @@ -324,7 +304,7 @@

    biocframeBiocFrame

    +
    Bioconductor-like data frames
    @@ -352,7 +332,7 @@

    biocframe +

    diff --git a/authors.html b/authors.html index b8a74b3..868bbd1 100644 --- a/authors.html +++ b/authors.html @@ -6,7 +6,7 @@ - Contributors - BiocFrame 0.4.1 documentation + Contributors - BiocFrame 0.5.0 documentation @@ -123,7 +123,7 @@
    -
    BiocFrame 0.4.1 documentation
     +
    BiocFrame 0.5.0 documentation
    @@ -146,7 +146,7 @@
    - BiocFrame 0.4.1 documentation + BiocFrame 0.5.0 documentation @@ -258,7 +258,7 @@

    Contributors +

    diff --git a/changelog.html b/changelog.html index 39fcea6..dc75d9e 100644 --- a/changelog.html +++ b/changelog.html @@ -6,7 +6,7 @@ - Changelog - BiocFrame 0.4.1 documentation + Changelog - BiocFrame 0.5.0 documentation @@ -123,7 +123,7 @@
    -
    BiocFrame 0.4.1 documentation
     +
    BiocFrame 0.5.0 documentation
    @@ -146,7 +146,7 @@
    - BiocFrame 0.4.1 documentation + BiocFrame 0.5.0 documentation @@ -203,8 +203,19 @@

    Changelog#

    -
    -

    Version 0.3 (development)#

    +
    +

    Version 0.5#

    +
      +

    • Bugfixes to avoid pass-by-reference effects when setting or removing columns.

      • +

    • Provide functional-style method to add/remove multiple columns at once.

      • +

    • Allow setting/removal of columns by position index instead of name.

      • +

    • Provide a relaxed_combine_rows and merge function for flexible combining.

      • +

    • Reduce the variety of arguments for __getitem__, to simplify user expectations.

      • +

    • Internal refactoring to use generics from the BiocUtils package.

      • +
    +
    +
    +

    Version 0.3#

    This release migrates the package to a more palatable Google’s Python style guide. A major modification to the package is with casing, all camelCase methods, functions and parameters are now snake_case.

    In addition, docstrings and documentation has been updated to use sphinx’s features of linking objects to their types. Sphinx now also documents private and special dunder methods (e.g. __getitem__, __copy__ etc). Intersphinx has been updated to link to references from dependent packages.

    configuration for flake8, ruff and black has been added to pyproject.toml and setup.cfg to be less annoying.

    @@ -276,7 +287,8 @@

    Version 0.1

    diff --git a/contributing.html b/contributing.html index 75758c8..2b4b1f7 100644 --- a/contributing.html +++ b/contributing.html @@ -6,7 +6,7 @@ - Contributing - BiocFrame 0.4.1 documentation + Contributing - BiocFrame 0.5.0 documentation @@ -123,7 +123,7 @@
    -
    BiocFrame 0.4.1 documentation
     +
    BiocFrame 0.5.0 documentation
    @@ -146,7 +146,7 @@
    - BiocFrame 0.4.1 documentation + BiocFrame 0.5.0 documentation @@ -522,7 +522,7 @@

    Releases

    -
    +
    diff --git a/genindex.html b/genindex.html index a2d735b..ed503f0 100644 --- a/genindex.html +++ b/genindex.html @@ -4,7 +4,7 @@ - Index - BiocFrame 0.4.1 documentation + Index - BiocFrame 0.5.0 documentation @@ -121,7 +121,7 @@
    -
    BiocFrame 0.4.1 documentation
     +
    BiocFrame 0.5.0 documentation
    @@ -144,7 +144,7 @@
    - BiocFrame 0.4.1 documentation + BiocFrame 0.5.0 documentation @@ -201,7 +201,7 @@

    Index

    -
    _ | B | C | D | F | G | H | I | L | M | N | O | R | S | T
    +
    _ | B | C | D | F | G | H | I | M | R | S | T

    _

    @@ -210,23 +210,17 @@

    _

  • __array_ufunc__() (biocframe.BiocFrame.BiocFrame method)
  • __copy__() (biocframe.BiocFrame.BiocFrame method) - -
  • __deepcopy__() (biocframe.BiocFrame.BiocFrame method) - -
  • __delitem__() (biocframe.BiocFrame.BiocFrame method)
  • __getitem__() (biocframe.BiocFrame.BiocFrame method) +
    • +
  • __init__() (biocframe.BiocFrame.BiocFrame method)
    • @@ -238,25 +232,13 @@

    _

  • __len__() (biocframe.BiocFrame.BiocFrame method) - -
  • __next__() (biocframe.BiocFrame.BiocFrameIter method)
  • __repr__() (biocframe.BiocFrame.BiocFrame method) - -
  • __setitem__() (biocframe.BiocFrame.BiocFrame method) - -
    • @@ -281,13 +263,8 @@

    B

  • module
    • -
  • - biocframe.Factor - -
    • + +
    • biocframe.io @@ -295,27 +272,11 @@

      B

    • module
    - -
    -
    +
    diff --git a/readme.html b/readme.html index 1f14a20..aa74a26 100644 --- a/readme.html +++ b/readme.html @@ -6,7 +6,7 @@ - BiocFrame - BiocFrame 0.4.1 documentation + Bioconductor-like data frames - BiocFrame 0.5.0 documentation @@ -123,7 +123,7 @@
    -
    BiocFrame 0.4.1 documentation
     +
    BiocFrame 0.5.0 documentation
    @@ -146,7 +146,7 @@
    - BiocFrame 0.4.1 documentation + BiocFrame 0.5.0 documentation @@ -215,26 +215,23 @@

    Project generated with PyScaffold PyPI-Server Unit tests

    -
    -

    BiocFrame#

    -

    This package provides

    -
      -

    • BiocFrame class, an alternative to Pandas DataFrame.

      -

      BiocFrame makes no assumption on the types of the columns, the minimum requirement is each column implements length: __len__ and slice: __getitem__ dunder methods. This allows BiocFrame to accept nested representations or any supported class as columns.

      -
      • -

    • Factor class, equivalent to R’s factor.

      -

      The aim is to encode a list of strings as integers for easier numerical analysis.

      -
      • -
    -

    To get started, install the package from PyPI

    +
    +

    Bioconductor-like data frames#

    +
    +

    Overview#

    +

    This package implements the BiocFrame class, a Bioconductor-friendly alternative to Pandas DataFrame. +The main advantage is that the BiocFrame makes no assumption on the types of the columns - +as long as an object has a length (__len__) and slicing methods (__getitem__), it can be used inside a BiocFrame. +This allows us to accept arbitrarily complex objects as columns, which is often the case in Bioconductor objects.

    +

    To get started, install the package from PyPI:

    pip install biocframe
    -
    -

    BiocFrame#

    +
    +
    +

    Construction#

    To construct a BiocFrame object, simply provide the data as a dictionary.

    -
    from random import random
-from biocframe import BiocFrame
+
    from biocframe import BiocFrame
 
 obj = {
     "ensembl": ["ENS00001", "ENS00002", "ENS00003"],
@@ -242,18 +239,16 @@ 
    BiocFrame#}
 bframe = BiocFrame(obj)
 print(bframe)
+## BiocFrame with 3 rows and 2 columns
+##      ensembl symbol
+##       <list> <list>
+## [0] ENS00001  MAP1A
+## [1] ENS00002   BIN1
+## [2] ENS00003   ESR1
 
    
 
    
-
    ## output
-BiocFrame with 3 rows and 2 columns
-    ensembl symbol
-    <list> <list>
-[0] ENS00001  MAP1A
-[1] ENS00002   BIN1
-[2] ENS00003   ESR1
-
    
-
    
-
    You can specify complex representations as columns, for example
    
+
    You can specify complex objects as columns, as long as they have some “length” equal to the number of rows.
+For example, we can nest a BiocFrame inside another BiocFrame:
    
 
    obj = {
     "ensembl": ["ENS00001", "ENS00002", "ENS00002"],
     "symbol": ["MAP1A", "BIN1", "ESR1"],
@@ -266,113 +261,173 @@ 
    BiocFrame#bframe2 = BiocFrame(obj, row_names=["row1", "row2", "row3"])
 print(bframe2)
+## BiocFrame with 3 rows and 3 columns
+##       ensembl symbol         ranges
+##        <list> <list>    <BiocFrame>
+## row1 ENS00001  MAP1A chr1:1000:1100
+## row2 ENS00002   BIN1 chr2:1100:4000
+## row3 ENS00002   ESR1 chr3:5000:5500
 
    
 
    
-
    ## output
-BiocFrame with 3 rows and 3 columns
-    ensembl symbol         ranges
-    <list> <list>    <BiocFrame>
-row1 ENS00001  MAP1A chr1:1000:1100
-row2 ENS00002   BIN1 chr2:1100:4000
-row3 ENS00002   ESR1 chr3:5000:5500
-
    
-
    
-
    
-
    Properties#
    
-
    Properties can be accessed directly from the object, for e.g. column names, row names and/or dimensions of the BiocFrame.
    
-
    # Dimensionality or shape
-print(bframe.shape)
-
-## output
+
    
+
    
+
    Extracting data#
    
+
    Properties can be accessed directly from the object:
    
+
    print(bframe.shape)
 ## (3, 2)
 
-# get the column names
-print(bframe.column_names)
+print(bframe.get_column_names())
+## ['ensembl', 'symbol']
 
-## output
+print(bframe.column_names) # same as above
 ## ['ensembl', 'symbol']
 
    
 
    
-
    
-
    Setters#
    
-
    To set various properties
    
-
    # set new column names
-bframe.column_names = ["column1", "column2"]
-print(bframe)
+
    We can fetch individual columns:
    
+
    bframe.get_column("ensembl")
+## ['ENS00001', 'ENS00002', 'ENS00003']
+
+bframe["ensembl"]
+## ['ENS00001', 'ENS00002', 'ENS00003']
 
    
 
    
-
    ## output
-BiocFrame with 3 rows and 2 columns
-    column1 column2
-    <list>  <list>
-[0] ENS00001   MAP1A
-[1] ENS00002    BIN1
-[2] ENS00003    ESR1
+
    And we can get individual rows as a dictionary:
    
+
    bframe.get_row(2)
+## {'ensembl': 'ENS00003', 'symbol': 'ESR1'}
 
    
 
    
-
    To add new columns,
    
-
    bframe["score"] = range(2, 5)
-print(bframe)
+
    To extract a subset of the data in the BiocFrame, we use the subset ([]) operator.
+This accepts different subsetting arguments like a boolean vector, a slice object, a sequence of indices, or row/column names.
    
+
    sliced = bframe[1:2, [True, False, False]]
+print(sliced)
+## BiocFrame with 1 row and 1 column
+##      column1
+##       <list>
+## [0] ENS00002
+
+sliced = bframe[[0,2], ["symbol", "ensembl"]]
+print(sliced)
+## BiocFrame with 2 rows and 2 columns
+##     symbol  ensembl
+##     <list>   <list>
+## [0]  MAP1A ENS00001
+## [1]   ESR1 ENS00003
+
+# Short-hand to get a single column:
+bframe["ensembl"]
+## ['ENS00001', 'ENS00002', 'ENS00003']
 
    
 
    
-
    ## output
-BiocFrame with 3 rows and 3 columns
-    column1 column2   score
-    <list>  <list> <range>
-[0] ENS00001   MAP1A       2
-[1] ENS00002    BIN1       3
-[2] ENS00003    ESR1       4
+
    
+
    
+
    Setting data#
    
+
    
+
    Preferred approach#
    
+
    To set BiocFrame properties, we encourage a functional style of programming that avoids mutating the object.
+This avoids inadvertent modification of BiocFrames that are part of larger data structures.
    
+
    modified = bframe.set_column_names(["column1", "column2"])
+print(modified)
+## BiocFrame with 3 rows and 2 columns
+##      column1 column2
+##       <list>  <list>
+## [0] ENS00001   MAP1A
+## [1] ENS00002    BIN1
+## [2] ENS00003    ESR1
+
+# Original is unchanged:
+print(bframe.get_column_names())
+## ['ensembl', 'symbol']
 
    
 
    
-
    
-
    Functional style#
    
-
    Properties can also be accessed or set using a functional approach
    
-
    To get column names,
    
-
    print(bframe.get_column_names())
+
    To add new columns, or replace existing columns:
    
+
    modified = bframe.set_column("symbol", ["A", "B", "C"])
+print(modified)
+## BiocFrame with 3 rows and 2 columns
+##      ensembl symbol
+##       <list> <list>
+## [0] ENS00001      A
+## [1] ENS00002      B
+## [2] ENS00003      C
 
-## output
-## ['ensembl', 'symbol']
+modified = bframe.set_column("new_col_name", range(2, 5))
+print(modified)
+## BiocFrame with 3 rows and 3 columns
+##      ensembl symbol new_col_name
+##       <list> <list>      <range>
+## [0] ENS00001  MAP1A            2
+## [1] ENS00002   BIN1            3
+## [2] ENS00003   ESR1            4
 
    
 
    
-
    To set new column names,
    
-
    # set new column names
-bframe.set_column_names(names = ["column1", "column2"], in_place=True)
-print(bframe)
+
    Change the row or column names:
    
+
    modified = bframe.\
+    set_column_names(["FOO", "BAR"]).\
+    set_row_names(['alpha', 'bravo', 'charlie'])
+print(modified)
+## BiocFrame with 3 rows and 2 columns
+##              FOO    BAR
+##           <list> <list>
+##   alpha ENS00001  MAP1A
+##   bravo ENS00002   BIN1
+## charlie ENS00003   ESR1
 
    
 
    
-
    ## output
-BiocFrame with 3 rows and 2 columns
-    column1 column2
-    <list>  <list>
-[0] ENS00001   MAP1A
-[1] ENS00002    BIN1
-[2] ENS00003    ESR1
+
    We also support Bioconductor’s metadata concepts, either along the columns or for the entire object:
    
+
    modified = bframe.\
+    set_metadata({ "author": "Jayaram Kancherla" }).\
+    set_column_data(BiocFrame({"column_source": ["Ensembl", "HGNC" ]}))
+print(modified)
+## BiocFrame with 3 rows and 2 columns
+##      ensembl symbol
+##       <list> <list>
+## [0] ENS00001  MAP1A
+## [1] ENS00002   BIN1
+## [2] ENS00003   ESR1
+## ------
+## column_data(1): column_source
+## metadata(1): author
 
    
 
    
-
    If in_place is True, we mutate the object, otherwise returns a new instance.
    
-
    
 
    
-
    
-
    
-
    Subset BiocFrame#
    
-
    Use the subset ([]) operator to slice the object,
    
-
    sliced = bframe[1:2, [True, False, False]]
-print(sliced)
+
    
+
    The other way#
    
+
    Properties can also be set by direct assignment for in-place modification.
+We prefer not to do it this way as it can silently mutate BiocFrame instances inside other data structures.
+Nonetheless:
    
+
    testframe = BiocFrame({ "A": [1,2,3], "B": [4,5,6] })
+testframe.column_names = ["column1", "column2" ]
+print(testframe)
+## BiocFrame with 3 rows and 2 columns
+##     column1 column2
+##      <list>  <list>
+## [0]       1       4
+## [1]       2       5
+## [2]       3       6
 
    
 
    
-
    ## output
-BiocFrame with 1 row and 1 column
-    column1
-    <list>
-[0] ENS00002
+
    Similarly, we could set or replace columns directly:
    
+
    testframe["column2"] = ["A", "B", "C"]
+testframe[1:3, ["column1","column2"]] = BiocFrame({"x":[4, 5], "y":["E", "F"]})
+## BiocFrame with 3 rows and 2 columns
+##     column1 column2
+##      <list>  <list>
+## [0]       1       A
+## [1]       4       E
+## [2]       5       F
 
    
 
    
-
    This operation accepts different slice input types, you can either specify a boolean vector, a slice object, a list of indices, or row/column names to subset.
    
+
    These assignments are the same as calling the corresponding set_*() methods with in_place = True.
+It is best to do this only if the BiocFrame object is not being used anywhere else;
+otherwise, it is safer to just create a (shallow) copy via the default in_place = False.
    
 
    
-
    
-
    Combine#
    
-
    BiocFrame implements the combine generic from biocgenerics. To combine multiple objects,
    
-
    bframe1 = BiocFrame(
+
    
+
    
+
    Combining objects#
    
+
    BiocFrame implements methods for the various combine generics from BiocUtils.
+So, for example, to combine by row:
    
+
    import biocutils
+
+bframe1 = BiocFrame(
     {
         "odd": [1, 3, 5, 7, 9],
         "even": [0, 2, 4, 6, 8],
@@ -386,56 +441,87 @@ 
    Combine#<
     }
 )
 
-from biocgenerics.combine import combine
-combined = combine(bframe1, bframe2)
-
-# OR an object oriented approach
-
-combined = bframe1.combine(bframe2)
+combined = biocutils.combine_rows(bframe1, bframe2)
+print(combined)
+## BiocFrame with 10 rows and 2 columns
+##        odd   even
+##     <list> <list>
+## [0]      1      0
+## [1]      3      2
+## [2]      5      4
+## [3]      7      6
+## [4]      9      8
+## [5]     11      0
+## [6]     33     22
+## [7]     55     44
+## [8]     77     66
+## [9]     99     88
 
    
 
    
-
    ## output
-BiocFrame with 10 rows and 2 columns
-    odd   even
-    <list> <list>
-[0]      1      0
-[1]      3      2
-[2]      5      4
-[3]      7      6
-[4]      9      8
-[5]     11      0
-[6]     33     22
-[7]     55     44
-[8]     77     66
-[9]     99     88
+
    Similarly, to combine by column:
    
+
    bframe3 = BiocFrame(
+    {
+        "foo": ["A", "B", "C", "D", "E"],
+        "bar": [True, False, True, False, True]
+    }
+)
+
+combined = biocutils.combine_columns(bframe1, bframe3)
+print(combined)
+BiocFrame with 5 rows and 4 columns
+       odd   even    foo    bar
+    <list> <list> <list> <list>
+[0]      1      0      A   True
+[1]      3      2      B  False
+[2]      5      4      C   True
+[3]      7      6      D  False
+[4]      9      8      E   True
 
    
 
    
-
    For more details, check out the BiocFrame class reference.
    
-
    
-
    
-
    
-
    Factor#
    
-
    Convert a list into a Factor object,
    
-
    from biocframe import Factor
-
-f1 = Factor.from_list(["A", "B", "A", "B", "E"])
-print(f1)
+
    By default, both methods above assume that the number and identity of columns (for combine_rows()) or rows (for combine_columns()) are the same across objects.
+If this is not the case, e.g., with different columns across objects, we can use BiocFrame’s relaxed_combine_rows() instead:
    
+
    from biocframe import relaxed_combine_rows
+modified2 = bframe2.set_column("foo", ["A", "B", "C", "D", "E"])
+combined = relaxed_combine_rows(bframe1, modified2)
+print(combined)
+## BiocFrame with 10 rows and 3 columns
+##        odd   even    foo
+##     <list> <list> <list>
+## [0]      1      0   None
+## [1]      3      2   None
+## [2]      5      4   None
+## [3]      7      6   None
+## [4]      9      8   None
+## [5]     11      0      A
+## [6]     33     22      B
+## [7]     55     44      C
+## [8]     77     66      D
+## [9]     99     88      E
 
    
 
    
-
    ## output
-Factor of length 5 with 3 levels
-values: ['A', 'B', 'A', 'B', 'E']
-levels: ['A', 'B', 'E']
-ordered: False
+
    Similarly, if the rows are different, we can use BiocFrame’s merge function:
    
+
    from biocframe import merge
+modified1 = bframe1.set_row_names(["A", "B", "C", "D", "E"])
+modified3 = bframe3.set_row_names(["C", "D", "E", "F", "G"])
+combined = merge([modified1, modified3], by=None, join="outer")
+## BiocFrame with 7 rows and 4 columns
+##      odd   even    foo    bar
+##   <list> <list> <list> <list>
+## A      1      0   None   None
+## B      3      2   None   None
+## C      5      4      A   True
+## D      7      6      B  False
+## E      9      8      C   True
+## F   None   None      D  False
+## G   None   None      E   True
 
    
 
    
-
    The Factor class behaves as a list and most operations to slice or replace should work here. Check out the docs for more information!
    
-
 
    
-
    
-
    Note#
    
-
    This project has been set up using PyScaffold 4.5. For details and usage
-information on PyScaffold see https://pyscaffold.org/.
    
+
    
+
    Further reading#
    
+
    Check out the reference documentation for more details.
    
+
    Also see check out Bioconductor’s S4Vectors package,
+which implements the DFrame class on which BiocFrame was based.
    
 
    
 
    
 
@@ -494,21 +580,17 @@ 
    Note#
           
    
             
    
-
    +
    diff --git a/search.html b/search.html index 5ba7b59..6f55659 100644 --- a/search.html +++ b/search.html @@ -4,7 +4,7 @@ - Search - BiocFrame 0.4.1 documentation + Search - BiocFrame 0.5.0 documentation @@ -120,7 +120,7 @@
    -
    BiocFrame 0.4.1 documentation
     +
    BiocFrame 0.5.0 documentation
    @@ -143,7 +143,7 @@
    - BiocFrame 0.4.1 documentation + BiocFrame 0.5.0 documentation @@ -240,7 +240,7 @@
    -
    +
    diff --git a/searchindex.js b/searchindex.js index ceeca45..3f67834 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["api/biocframe", "api/biocframe.io", "api/modules", "authors", "changelog", "contributing", "index", "license", "readme"], "filenames": ["api/biocframe.rst", "api/biocframe.io.rst", "api/modules.rst", "authors.md", "changelog.md", "contributing.md", "index.md", "license.md", "readme.md"], "titles": ["biocframe package", "biocframe.io package", "biocframe", "Contributors", "Changelog", "Contributing", "BiocFrame", "License", "BiocFrame"], "terms": {"io": [0, 2, 8], "from_panda": [0, 2], "class": [0, 4, 5, 8], "data": [0, 1, 2, 6, 8], "none": 0, "number_of_row": [0, 2], "row_nam": [0, 2, 8], "column_nam": [0, 2, 8], "mcol": [0, 2], "metadata": [0, 2], "sourc": [0, 1, 5], "base": [0, 4, 5], "object": [0, 1, 4, 8], "i": [0, 1, 4, 5, 6, 7, 8], "an": [0, 7, 8], "altern": [0, 8], "datafram": [0, 1, 4, 6, 8], "support": [0, 6, 8], 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