Matrix Data Wrangling

Introduction

There are several scenarios where you would want to wrangle a Matrix by subsetting or reordering or changing columns, etc. Here are some examples. —-

Subset a PAM for a Taxon or Group of Taxa and Export to GeoJSON

You can subset a PAM for one ore more taxa using a data wrangler and then create GeoJSON for the subset Matrix.

>>> import json
>>> from lmpy.matrix import Matrix
>>> from lmpy.spatial.geojsonify import geojsonify_matrix
>>> from lmpy.data_wrangling.matrix.subset_reorder_slices_wrangler import SubsetReorderSlicesWrangler
>>> pam = Matrix.load('my_pam.lmm')
>>> keep_taxa = ['Species A', 'Species B', 'Species R']
>>> wrangler = SubsetReorderSlicesWrangler(axes={'1': keep_taxa})
>>> subset_pam = wrangler.wrangle_matrix(pam)
>>> # create GeoJSON for subset PAM
>>> subset_geojson = geojsonify_matrix(subset_pam, resolution=0.5, omit_values=[0])
>>> with open('subset_pam.geojson', mode='wt') as out_json:
>>>     out_json.dump(subset_geojson, out_json)

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Subset a Matrix by Taxa, Generate Stats, and Write GeoJSON

You can subset a PAM by taxa, generate stats, and then write the outputs to a GeoJSON file for spatial inspection using data wranglers and PamStats.

>>> import json
>>> from lmpy.matrix import Matrix
>>> from lmpy.spatial.geojsonify import geojsonify_matrix
>>> from lmpy.statistics.pam_stats import PamStats
>>> from lmpy.data_wrangling.matrix.purge_empty_slices_wrangler import PurgeEmptySlicesWrangler
>>> from lmpy.data_wrangling.matrix.subset_reorder_slices_wrangler import SubsetReorderSlicesWrangler
>>> pam = Matrix.load('my_pam.lmm')
>>> keep_taxa = ['Species A', 'Species B', 'Species R']
>>> # Set up wranlgers, first subset by species, then purge empty rows
>>> wranglers = [
...     SubsetReorderSlicesWrangler(axes={'1': keep_taxa}),
...     PurgeEmptySlicesWrangler(purge_axes=[0])
... ]
>>> # Wrangle the matrix using each of the wranglers
>>> wrangled_pam = pam
>>> for wrangler in wranglers:
...     wrangled_pam = wrangler.wrangle_matrix(pam)
>>> # Create PamStats for the subset matrix
>>> site_stats = PamStats(wrangled_pam).calculate_site_statistics()
>>> # create GeoJSON for the site statistics
>>> stats_geojson = geojsonify_matrix(site_stats, resolution=0.5, omit_values=[0])
>>> with open('site_stats.geojson', mode='wt') as out_json:
>>>     out_json.dump(stats_geojson, out_json)