]) \
.with_normalization(Normalization("CLR", "CLR")) \
.with_pair_strategy("paired_subtract_sex_balanced") \
.with_metadata_filter([
None,
MetadataFilter(
"Off Treatment",
"treatment_status",
["Off", "Control"]
)
])
woltka_species = AnalysisFactory(
[BiomTable("species")],
metadata_filepath,
"All Species",
).with_normalization(Normalization("CLR", "CLR")) \
.with_pair_strategy("paired_subtract_sex_balanced")
return MultiFactory([woltka_species, woltka_transforms])
if __name__ == "__main__":
# Pretend all scripts are run from root of repo for file paths.
import os
os.chdir("..")
DryRunner().run(configure())
SerialRunner().run(configure())
.with_normalization([Normalization("CLR", "CLR")])\
.with_feature_set([fset_species] + fset_species.create_univariate_sets() + fsets)
probstel_lda = AnalysisFactory(
BiomTable("genus"),
metadata_filepath
)\
.with_lda(1)\
.with_pair_strategy(["paired_subtract_sex_balanced"])\
.with_normalization([Normalization("CLR", "CLR")])\
.with_feature_set([probstel] + probstel.create_univariate_sets())
# return MultiFactory([
# # umap,
# lda,
# # pca,
# # raw,
# ])
# return probstel_lda
return MultiFactory([raw, probstel_lda])
if __name__ == "__main__":
# Pretend all scripts are run from root of repo for file paths.
import os
os.chdir("..")
runner = SerialRunner()
lda_plot = LDAPlot(rows=2)
lda_plot.hook_events(runner)
runner.run(configure())
lda_plot.print_acc()