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re-nest Pipelines (#27)
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fixes #22
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@Oddant1
Oddant1 authored Nov 7, 2024
1 parent 905b39b commit 21f97b8
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Showing 4 changed files with 75 additions and 91 deletions.
60 changes: 25 additions & 35 deletions q2_boots/_alpha.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,12 +10,8 @@

import pandas as pd

from q2_diversity import (alpha as q2div_alpha,
alpha_phylogenetic as q2div_alpha_phylogenetic)
from q2_diversity_lib.alpha import METRICS

from q2_boots._resample import resample


def alpha_average(data: pd.Series, average_method: str) -> pd.Series:
if average_method == "median":
Expand All @@ -35,32 +31,28 @@ def alpha_collection(ctx, table, sampling_depth, metric, n,
replacement, phylogeny=None):
_validate_alpha_metric(metric, phylogeny)

resample_function = resample
alpha_metric_function = _get_alpha_metric_function(ctx, metric, phylogeny)

tables = resample_function(ctx=ctx,
table=table,
sampling_depth=sampling_depth,
n=n,
replacement=replacement)
resample_action = ctx.get_action("boots", "resample")
alpha_metric_action = _get_alpha_metric_action(ctx, metric, phylogeny)

results = _alpha_collection_from_tables(tables, alpha_metric_function)
tables, = resample_action(table=table,
sampling_depth=sampling_depth,
n=n,
replacement=replacement)

results = _alpha_collection_from_tables(tables, alpha_metric_action)
return results


def alpha(ctx, table, sampling_depth, metric, n, replacement, phylogeny=None,
average_method='median'):

alpha_collection_function = alpha_collection
alpha_collection_action = ctx.get_action("boots", "alpha_collection")
alpha_average_action = ctx.get_action('boots', 'alpha_average')
sample_data = alpha_collection_function(ctx=ctx,
table=table,
sampling_depth=sampling_depth,
phylogeny=phylogeny,
metric=metric,
n=n,
replacement=replacement)
sample_data, = alpha_collection_action(table=table,
sampling_depth=sampling_depth,
phylogeny=phylogeny,
metric=metric,
n=n,
replacement=replacement)

result, = alpha_average_action(sample_data, average_method)
return result
Expand All @@ -71,27 +63,25 @@ def _validate_alpha_metric(metric, phylogeny):
raise ValueError(f'Metric {metric} requires a phylogenetic tree.')


def _get_alpha_metric_function(ctx, metric, phylogeny):
def _get_alpha_metric_action(ctx, metric, phylogeny):
if _is_phylogenetic_alpha_metric(metric):
alpha_metric_function = q2div_alpha_phylogenetic
alpha_metric_function = functools.partial(alpha_metric_function,
ctx=ctx,
phylogeny=phylogeny,
metric=metric)
alpha_metric_action = ctx.get_action("diversity", "alpha_phylogenetic")
alpha_metric_action = functools.partial(alpha_metric_action,
phylogeny=phylogeny,
metric=metric)
else:
alpha_metric_function = q2div_alpha
alpha_metric_function = functools.partial(alpha_metric_function,
ctx=ctx,
metric=metric)
return alpha_metric_function
alpha_metric_action = ctx.get_action("diversity", "alpha")
alpha_metric_action = functools.partial(alpha_metric_action,
metric=metric)
return alpha_metric_action


def _is_phylogenetic_alpha_metric(metric):
return metric in (METRICS['PHYLO']['IMPL'] | METRICS['PHYLO']['UNIMPL'])


def _alpha_collection_from_tables(tables, alpha_metric_function):
def _alpha_collection_from_tables(tables, alpha_metric_action):
results = []
for table in tables.values():
results.append(alpha_metric_function(table=table))
results.append(alpha_metric_action(table=table)[0])
return results
69 changes: 33 additions & 36 deletions q2_boots/_beta.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,12 +13,8 @@
import skbio
from hdmedians import medoid

from q2_diversity import (beta as q2div_beta,
beta_phylogenetic as q2div_beta_phylogenetic)
from q2_diversity_lib.beta import METRICS

from q2_boots._resample import resample

_METRIC_MOD_DEFAULTS = {
'bypass_tips': False,
'pseudocount': 1,
Expand Down Expand Up @@ -58,17 +54,16 @@ def beta_collection(
variance_adjusted=_METRIC_MOD_DEFAULTS['variance_adjusted']):
_validate_beta_metric(metric, phylogeny)

resample_function = resample
beta_metric_function = _get_beta_metric_function(
resample_action = ctx.get_action("boots", "resample")
beta_metric_action = _get_beta_metric_action(
ctx, metric, phylogeny, bypass_tips, pseudocount, alpha,
variance_adjusted)

tables = resample_function(ctx=ctx,
table=table,
sampling_depth=sampling_depth,
n=n,
replacement=replacement)
results = _beta_collection_from_tables(tables, beta_metric_function)
tables, = resample_action(table=table,
sampling_depth=sampling_depth,
n=n,
replacement=replacement)
results = _beta_collection_from_tables(tables, beta_metric_action)

return results

Expand All @@ -79,19 +74,18 @@ def beta(ctx, table, metric, sampling_depth, n, replacement,
pseudocount=_METRIC_MOD_DEFAULTS['pseudocount'],
alpha=_METRIC_MOD_DEFAULTS['alpha'],
variance_adjusted=_METRIC_MOD_DEFAULTS['variance_adjusted']):
beta_collection_function = beta_collection
beta_collection_action = ctx.get_action('boots', 'beta_collection')
beta_average_action = ctx.get_action('boots', 'beta_average')
dms = beta_collection_function(ctx=ctx,
table=table,
phylogeny=phylogeny,
metric=metric,
sampling_depth=sampling_depth,
n=n,
pseudocount=pseudocount,
replacement=replacement,
variance_adjusted=variance_adjusted,
alpha=alpha,
bypass_tips=bypass_tips)
dms, = beta_collection_action(table=table,
phylogeny=phylogeny,
metric=metric,
sampling_depth=sampling_depth,
n=n,
pseudocount=pseudocount,
replacement=replacement,
variance_adjusted=variance_adjusted,
alpha=alpha,
bypass_tips=bypass_tips)

result, = beta_average_action(dms, average_method)
return result
Expand Down Expand Up @@ -129,32 +123,35 @@ def _validate_beta_metric(metric, phylogeny):
raise ValueError(f'Metric {metric} requires a phylogenetic tree.')


def _get_beta_metric_function(
def _get_beta_metric_action(
ctx, metric, phylogeny,
bypass_tips=_METRIC_MOD_DEFAULTS['bypass_tips'],
pseudocount=_METRIC_MOD_DEFAULTS['pseudocount'],
alpha=_METRIC_MOD_DEFAULTS['alpha'],
variance_adjusted=_METRIC_MOD_DEFAULTS['variance_adjusted']):
if _is_phylogenetic_beta_metric(metric):
beta_metric_function = q2div_beta_phylogenetic
beta_metric_function = functools.partial(
beta_metric_function, ctx=ctx, phylogeny=phylogeny, metric=metric,
bypass_tips=bypass_tips, alpha=alpha,
beta_metric_action = ctx.get_action("diversity", "beta_phylogenetic")
beta_metric_action = functools.partial(
beta_metric_action,
phylogeny=phylogeny,
metric=metric,
bypass_tips=bypass_tips,
alpha=alpha,
variance_adjusted=variance_adjusted)
else:
beta_metric_function = q2div_beta
beta_metric_function = functools.partial(
beta_metric_function, ctx=ctx, metric=metric,
pseudocount=pseudocount)
return beta_metric_function
beta_metric_action = ctx.get_action("diversity", "beta")
beta_metric_action = functools.partial(beta_metric_action,
metric=metric,
pseudocount=pseudocount)
return beta_metric_action


def _is_phylogenetic_beta_metric(metric):
return metric in METRICS['PHYLO']['IMPL'] | METRICS['PHYLO']['UNIMPL']


def _beta_collection_from_tables(tables, beta_metric_function):
def _beta_collection_from_tables(tables, beta_metric_action):
results = []
for table in tables.values():
results.append(beta_metric_function(table=table))
results.append(beta_metric_action(table=table)[0])
return results
31 changes: 14 additions & 17 deletions q2_boots/_core_metrics.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,20 +6,17 @@
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------

from q2_boots._resample import resample
from q2_boots._alpha import (_validate_alpha_metric,
_get_alpha_metric_function,
from q2_boots._alpha import (_validate_alpha_metric, _get_alpha_metric_action,
_alpha_collection_from_tables)
from q2_boots._beta import (_validate_beta_metric,
_get_beta_metric_function,
from q2_boots._beta import (_validate_beta_metric, _get_beta_metric_action,
_beta_collection_from_tables)


def core_metrics(ctx, table, sampling_depth, metadata, n, replacement,
phylogeny=None, alpha_average_method='median',
beta_average_method='non-metric-median'):

resample_function = resample
resample_action = ctx.get_action('boots', 'resample')
alpha_average_action = ctx.get_action('boots', 'alpha_average')
beta_average_action = ctx.get_action('boots', 'beta_average')
pcoa_action = ctx.get_action('diversity', 'pcoa')
Expand All @@ -37,28 +34,27 @@ def core_metrics(ctx, table, sampling_depth, metadata, n, replacement,
for beta_metric in beta_metrics:
_validate_beta_metric(beta_metric, phylogeny)

resampled_tables = resample_function(ctx=ctx,
table=table,
sampling_depth=sampling_depth,
n=n,
replacement=replacement)
resampled_tables, = resample_action(table=table,
sampling_depth=sampling_depth,
n=n,
replacement=replacement)

alpha_vectors = {}
for alpha_metric in alpha_metrics:
alpha_metric_function = _get_alpha_metric_function(
alpha_metric_action = _get_alpha_metric_action(
ctx, alpha_metric, phylogeny)
alpha_collection = _alpha_collection_from_tables(
resampled_tables, alpha_metric_function)
resampled_tables, alpha_metric_action)
avg_alpha_vector, = alpha_average_action(
alpha_collection, alpha_average_method)
alpha_vectors[alpha_metric] = avg_alpha_vector

beta_dms = {}
for beta_metric in beta_metrics:
beta_metric_function = _get_beta_metric_function(
beta_metric_action = _get_beta_metric_action(
ctx, beta_metric, phylogeny)
beta_collection = _beta_collection_from_tables(
resampled_tables, beta_metric_function)
resampled_tables, beta_metric_action)
avg_beta_dm, = beta_average_action(
beta_collection, beta_average_method)
beta_dms[beta_metric] = avg_beta_dm
Expand All @@ -68,7 +64,8 @@ def core_metrics(ctx, table, sampling_depth, metadata, n, replacement,
for key, dm in beta_dms.items():
pcoa_results, = pcoa_action(dm)
pcoas[key] = pcoa_results
emperor_plots[key] = emperor_plot_action(pcoa=pcoa_results,
metadata=metadata)[0]
emperor_plot, = emperor_plot_action(pcoa=pcoa_results,
metadata=metadata)
emperor_plots[key] = emperor_plot

return resampled_tables, alpha_vectors, beta_dms, pcoas, emperor_plots
6 changes: 3 additions & 3 deletions q2_boots/_resample.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,9 +11,9 @@ def resample(ctx, table, sampling_depth, n, replacement):
resampled_tables = []

for i in range(n):
resampled_table = rarefy_action(table=table,
sampling_depth=sampling_depth,
with_replacement=replacement)[0]
resampled_table, = rarefy_action(table=table,
sampling_depth=sampling_depth,
with_replacement=replacement)
resampled_tables.append(resampled_table)

return {f'resampled-table-{i}': t for i, t in enumerate(resampled_tables)}

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