FrequencyTable¶

class FrequencyTable(frequency, skipcols=None, allow_nan=False, **kwargs)[source]¶

An essential class for handling frequency data.

Parameters

frequency (Union[pandas.core.frame.DataFrame, str]) – Data containing frequency data.
skipcols (Union[Sequence[Union[int, str]], str, int]) – Columns to skip when processing data.
allow_nan (bool) – Allow NA/NaN values or raise an error.
kwargs – Remaining parameters passed to read_csv() or biom loader

Attributes

`any_nan`	Is there nan values present?
`controller`	Active essentials controller instance.
`data`	Pandas dataframe of FrequencyTable
`is_buckled`	Is current essentials instance is mounted or not.
`is_mounted`	True if current essentials instance is mounted or not.
`metadata`	The essential instance metadata.
`name`	The essential instance name.
`shape`	Return the shape/size of the essential instance.
`xrid`	Feature axis.
`xsid`	Sample axis.

Methods

`copy`()	Copy of the instance.
`drop_features_by_id`(ids)	Drop features by ids
`drop_features_without_counts`()	Drop features that has no counts.
`drop_samples_by_id`(ids)	Drop samples by ids
`export`(output_fp, *args[, _add_ext, sep])	Exports the sample metadata content into the specified file.
`from_biom`(filepath, **kwargs)	Factory method to construct a `FrequencyTable` from `biom` file.
`from_csv`(filepath, **kwargs)	Factory method to construct a `FrequencyTable` from CSV file.
`get_feature_ids`([dtype])	This function and its sample twin is a rescue method to fix RepPhylogeny index problem.
`get_sample_ids`([dtype])	This function and its sample twin is a rescue method to fix RepPhylogeny index problem.
`get_subset`([rids, sids])	Get subset of the `FrequencyTable`.
`merge_features_by_map`(mapping[, aggfunc])	Merge features by mapping
`merge_samples_by_map`(mapping[, aggfunc])	Merge samples by mapping
`rename_samples`(mapper)	Rename sample names.
`replace_nan_with`(value)	Replace NaN values with value.
`transform_to_relative_abundance`()	Transform absolute counts to relative.