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NF: Allow passing an AFQDataset object as input. #113

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merged 4 commits into from
May 10, 2022
Merged

NF: Allow passing an AFQDataset object as input. #113

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2ada466
NF: Allow passing a AFQDataset object as input.
arokem May 10, 2022
2f0d6a0
Add more documentation about this feature change.
arokem May 10, 2022
8404dbd
flake8 fix.
arokem May 10, 2022
22254c9
isinstance expects its inputs in the opposite order.
arokem May 10, 2022
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34 changes: 27 additions & 7 deletions afqinsight/plot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
from tqdm.auto import tqdm

from .utils import BUNDLE_MAT_2_PYTHON
from .datasets import AFQDataset


POSITIONS = OrderedDict(
Expand Down Expand Up @@ -52,8 +53,8 @@

def plot_tract_profiles(
X,
groups,
group_names,
groups=None,
group_names=None,
group_by=None,
group_by_name=None,
bins=None,
Expand All @@ -71,15 +72,18 @@ def plot_tract_profiles(

Parameters
----------
X : numpy.ndarray
matrix of tractometry features with shape (n_subjects, n_features).
X : numpy.ndarray or AFQDataset class instance
If array, this is a matrix of tractometry features with shape (n_subjects, n_features).

groups : list of numpy.ndarray
feature indices for each feature group of ``X``
groups : list of numpy.ndarray, optional
feature indices for each feature group of ``X``.
Must be provided if ``X`` is an array. Should not be provided if
``X`` is an AFQDataset.

group_names : list of tuples
the multi-indexed name for each group in ``groups``. Must be of same
length as ``groups``.
length as ``groups``. Must be provided if ``X`` is an array.
Should not be provided if ``X`` is an AFQDataset

group_by : list-like
grouping variable that will produce different bundle profiles with
Expand Down Expand Up @@ -142,6 +146,22 @@ def plot_tract_profiles(
dictionary of matplotlib figures, with keys corresponding to the
different diffusion metrics
"""
if isinstance(X, AFQDataset):
if groups is not None or group_names is not None:
raise ValueError(
"You provided an AFQDataset class instance as `X` input and also a `groups` or `group_names` input, but these are mutually exclusive."
)
# Allocate the variables needed below based on the input dataset:
group_names = X.group_names
groups = X.groups
X = X.X

else:
if groups is None or group_names is None:
raise ValueError(
"You provided an array input as `X` but did not provide both a `groups` and a `group_names` input. You must provide both of these for array input. "
)

plt_positions = subplot_positions if subplot_positions is not None else POSITIONS

if bins is not None and quantiles is not None:
Expand Down