| Parameters: |
- data_file (str) – file path to the biom table.
- sample_metadata_file (None or str, optional) – None (default) to just use sample names (no additional metadata).
if not None, file path to the sample metadata (aka mapping file in QIIME).
- feature_metadata_file (None or str, optional) – file path to the feature metadata.
- description (str) – description of the experiment
- sparse (bool) – read the biom table into sparse or dense array
- data_file_type (str, optional) – the data_file format. options:
‘biom’ : a biom table (biom-format.org) (default)
‘tsv’: a tab-separated table with (samples in column and feature in row)
‘openms’ : an OpenMS bucket table csv (rows are feature, columns are samples)
‘openms_transpose’ an OpenMS bucket table csv (columns are feature, rows are samples)
‘gnps_ms’ : an OpenMS bucket table tsv with samples as columns (exported from GNPS)
‘qiime2’ : a qiime2 biom table artifact (need to have qiime2 installed)
- feature_metadata_kwargs (sample_metadata_kwargs,) – keyword arguments passing to
pandas.read_table() when reading sample metadata
or feature metadata. For example, you can set sample_metadata_kwargs={'dtype':
{'ph': int}, 'encoding': 'latin-8'} to read the column of ph in the sample metadata
as int and parse the file as latin-8 instead of utf-8. By default, it assumes the first column in
the metadata files is sample/feature IDs and is read in as row index. To avoid this, please provide
{‘index_col’: False}.
- cls (
class, optional) – what class object to read the data into (Experiment by default)
- table_sample_id_proc (None or callable, optional) –
- table_feature_id_proc (None or callable, optional) – if not None, modify each sample/feature id in the table using the callable function.
The callable accepts a list of str and returns a list of str (sample/feature ids after processing).
Useful in metabolomics experiments, where the sampleIDs in the data table contain additional information compared to the
mapping file (using a ‘_’ separator), and this needs to be removed in order to sync the sampleIDs between table and mapping file.
- sample_in_row (bool, optional) – False if data table columns are sample, True if rows are samples
- normalize (int or None) – normalize each sample to the specified read count.
None to not normalize
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