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[ENH 🏝] bug fixes in load_summary_stats and v1.0.3
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@saratheriver
saratheriver committed Feb 25, 2021
1 parent 8fcaf4d commit 7f3266e
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Showing 5 changed files with 118 additions and 3 deletions.
2 changes: 1 addition & 1 deletion docs/pages/01.install/index.rst
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Expand Up @@ -35,7 +35,7 @@ Installation

**ENIGMA TOOLBOX** was tested with MATLAB R2017b.

To install the MATLAB toolbox simply `download <https://github.com/MICA-MNI/ENIGMA/archive/1.0.2.zip>`_
To install the MATLAB toolbox simply `download <https://github.com/MICA-MNI/ENIGMA/archive/1.0.3.zip>`_
and unzip the GitHub toolbox (slow 🐢) or run the following command in your terminal (fast 🐅): ::
git clone https://github.com/MICA-MNI/ENIGMA.git
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11 changes: 11 additions & 0 deletions docs/pages/02.whatsnew/index.rst
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Expand Up @@ -5,6 +5,16 @@
What's new?
======================================

v1.0.3 (February 25, 2021)
------------------------------------------
OCD subcortical volume measures were not loading when using ``load_summary_stats('ocd')``; this issue is now resolved.

::

↪ [ENH 🔧] Fix OCD sctx summary stats loading issue | @saratheriver
↪ [DOC 📄] Update documentations | @saratheriver


v1.0.2 (February 23, 2021)
------------------------------------------
Bug fixes in the ``fetch_ahba`` function. Users who wish to use this function (or have used it in a previous version)
Expand All @@ -16,6 +26,7 @@ must update their **ENIGMA Toolbox** to this release; ``fetch_ahba`` from previo
↪ [ENH 🔧] Fix bug and replace stable gene lists | @saratheriver
↪ [DOC 📄] Update documentations | @saratheriver


v1.0.1 (January 11, 2021)
------------------------------------------
Bug fixes and improvement
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2 changes: 1 addition & 1 deletion enigmatoolbox/_version.py
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@@ -1,3 +1,3 @@
"""enigmatoolbox version"""

__version__ = '1.0.2'
__version__ = '1.0.3'
87 changes: 86 additions & 1 deletion enigmatoolbox/datasets/base.py
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Expand Up @@ -860,6 +860,74 @@ def load_summary_stats(disorder=None):
CortSurf_medicatedcase_controls_pediatric = pd.read_csv(os.path.join(root_pth, 'summary_statistics',
'ocdpediatric_medicatedcase-controls_CortSurf.csv'),
error_bad_lines=False)
SubVol_case_vs_controls_adult = pd.read_csv(os.path.join(root_pth,
'summary_statistics',
'ocdadult_case-controls_SubVol.csv'),
error_bad_lines=False)
SubVol_medicatedcase_vs_controls_adult = pd.read_csv(os.path.join(root_pth,
'summary_statistics',
'ocdadult_medicatedcase-controls_SubVol.csv'),
error_bad_lines=False)
SubVol_unmedicatedcase_vs_controls_adult = pd.read_csv(os.path.join(root_pth,
'summary_statistics',
'ocdadult_unmedicatedcase-controls_SubVol.csv'),
error_bad_lines=False)
SubVol_medicatedcase_vs_unmedicated_adult = pd.read_csv(os.path.join(root_pth,
'summary_statistics',
'ocdadult_medicatedcase-unmedicatedcase_SubVol.csv'),
error_bad_lines=False)
SubVol_case_vs_controls_adult_late = pd.read_csv(os.path.join(root_pth,
'summary_statistics',
'ocdadult_case-controls_SubVol_late.csv'),
error_bad_lines=False)
SubVol_case_vs_controls_adult_early = pd.read_csv(os.path.join(root_pth,
'summary_statistics',
'ocdadult_case-controls_SubVol_early.csv'),
error_bad_lines=False)
SubVol_late_vs_early_adult = pd.read_csv(os.path.join(root_pth,
'summary_statistics',
'ocdadult_late-early_SubVol.csv'),
error_bad_lines=False)
SubVol_case_vs_controls_adult_depression = pd.read_csv(os.path.join(root_pth,
'summary_statistics',
'ocdadult_case-controls_SubVol_depression.csv'),
error_bad_lines=False)
SubVol_case_vs_controls_adult_nodepression = pd.read_csv(os.path.join(root_pth,
'summary_statistics',
'ocdadult_case-controls_SubVol_nodepression.csv'),
error_bad_lines=False)
SubVol_depression_vs_nodepression_adult = pd.read_csv(os.path.join(root_pth,
'summary_statistics',
'ocdadult_depression-nodepression_SubVol.csv'),
error_bad_lines=False)
SubVol_case_vs_controls_adult_anxiety = pd.read_csv(os.path.join(root_pth,
'summary_statistics',
'ocdadult_case-controls_SubVol_anxiety.csv'),
error_bad_lines=False)
SubVol_case_vs_controls_adult_noanxiety = pd.read_csv(os.path.join(root_pth,
'summary_statistics',
'ocdadult_case-controls_SubVol_noanxiety.csv'),
error_bad_lines=False)
SubVol_anxiety_vs_noanxiety_adult = pd.read_csv(os.path.join(root_pth,
'summary_statistics',
'ocdadult_anxiety-noanxiety_SubVol.csv'),
error_bad_lines=False)
SubVol_case_vs_controls_pediatric = pd.read_csv(os.path.join(root_pth,
'summary_statistics',
'ocdpediatric_case-controls_SubVol.csv'),
error_bad_lines=False)
SubVol_medicatedcase_vs_controls_pediatric = pd.read_csv(os.path.join(root_pth,
'summary_statistics',
'ocdpediatric_medicatedcase-controls_SubVol.csv'),
error_bad_lines=False)
SubVol_unmedicatedcase_vs_controls_pediatric = pd.read_csv(os.path.join(root_pth,
'summary_statistics',
'ocdpediatric_unmedicatedcase-controls_SubVol.csv'),
error_bad_lines=False)
SubVol_medicatedcase_vs_unmedicated_pediatric = pd.read_csv(os.path.join(root_pth,
'summary_statistics',
'ocdpediatric_medicatedcase-unmedicatedcase_SubVol.csv'),
error_bad_lines=False)

return {'CortThick_case_vs_controls_adult': CortThick_case_controls_adult,
'CortSurf_case_vs_controls_adult': CortSurf_case_controls_adult,
Expand All @@ -868,7 +936,24 @@ def load_summary_stats(disorder=None):
'CortThick_case_vs_controls_pediatric': CortThick_case_controls_pediatric,
'CortSurf_case_vs_controls_pediatric': CortSurf_case_controls_pediatric,
'CortThick_medicatedcase_vs_controls_pediatric': CortThick_medicatedcase_controls_pediatric,
'CortSurf_medicatedcase_vs_controls_pediatric': CortSurf_medicatedcase_controls_pediatric}
'CortSurf_medicatedcase_vs_controls_pediatric': CortSurf_medicatedcase_controls_pediatric,
'SubVol_case_vs_controls_adult': SubVol_case_vs_controls_adult,
'SubVol_medicatedcase_vs_controls_adult': SubVol_medicatedcase_vs_controls_adult,
'SubVol_unmedicatedcase_vs_controls_adult': SubVol_unmedicatedcase_vs_controls_adult,
'SubVol_medicatedcase_vs_unmedicated_adult': SubVol_medicatedcase_vs_unmedicated_adult,
'SubVol_case_vs_controls_adult_late': SubVol_case_vs_controls_adult_late,
'SubVol_case_vs_controls_adult_early': SubVol_case_vs_controls_adult_early,
'SubVol_late_vs_early_adult': SubVol_late_vs_early_adult,
'SubVol_case_vs_controls_adult_depression': SubVol_case_vs_controls_adult_depression,
'SubVol_case_vs_controls_adult_nodepression': SubVol_case_vs_controls_adult_nodepression,
'SubVol_depression_vs_nodepression_adult': SubVol_depression_vs_nodepression_adult,
'SubVol_case_vs_controls_adult_anxiety': SubVol_case_vs_controls_adult_anxiety,
'SubVol_case_vs_controls_adult_noanxiety': SubVol_case_vs_controls_adult_noanxiety,
'SubVol_anxiety_vs_noanxiety_adult': SubVol_anxiety_vs_noanxiety_adult,
'SubVol_case_vs_controls_pediatric': SubVol_case_vs_controls_pediatric,
'SubVol_medicatedcase_vs_controls_pediatric': SubVol_medicatedcase_vs_controls_pediatric,
'SubVol_unmedicatedcase_vs_controls_pediatric': SubVol_unmedicatedcase_vs_controls_pediatric,
'SubVol_medicatedcase_vs_unmedicated_pediatric': SubVol_medicatedcase_vs_unmedicated_pediatric}

elif disorder is "schizophrenia":
CortThick_case_controls = pd.read_csv(os.path.join(root_pth, 'summary_statistics',
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19 changes: 19 additions & 0 deletions matlab/scripts/summary_statistics/load_summary_stats.m
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Expand Up @@ -118,6 +118,25 @@
summary_stats.CortSurf_case_vs_controls_pediatric = readtable('ocdpediatric_case-controls_CortSurf.csv');
summary_stats.CortThick_medicatedcase_vs_controls_pediatric = readtable('ocdpediatric_medicatedcase-controls_CortThick.csv');
summary_stats.CortSurf_medicatedcase_vs_controls_pediatric = readtable('ocdpediatric_medicatedcase-controls_CortSurf.csv');

summary_stats.SubVol_case_vs_controls_adult = readtable('ocdadult_case-controls_SubVol.csv');
summary_stats.SubVol_medicatedcase_vs_controls_adult = readtable('ocdadult_medicatedcase-controls_SubVol.csv');
summary_stats.SubVol_unmedicatedcase_vs_controls_adult = readtable('ocdadult_unmedicatedcase-controls_SubVol.csv');
summary_stats.SubVol_medicatedcase_vs_unmedicated_adult = readtable('ocdadult_medicatedcase-unmedicatedcase_SubVol.csv');
summary_stats.SubVol_case_vs_controls_adult_late = readtable('ocdadult_case-controls_SubVol_late.csv');
summary_stats.SubVol_case_vs_controls_adult_early = readtable('ocdadult_case-controls_SubVol_early.csv');
summary_stats.SubVol_late_vs_early_adult = readtable('ocdadult_late-early_SubVol.csv');
summary_stats.SubVol_case_vs_controls_adult_depression = readtable('ocdadult_case-controls_SubVol_depression.csv');
summary_stats.SubVol_case_vs_controls_adult_nodepression = readtable('ocdadult_case-controls_SubVol_nodepression.csv');
summary_stats.SubVol_depression_vs_nodepression_adult = readtable('ocdadult_depression-nodepression_SubVol.csv');
summary_stats.SubVol_case_vs_controls_adult_anxiety = readtable('ocdadult_case-controls_SubVol_anxiety.csv');
summary_stats.SubVol_case_vs_controls_adult_noanxiety = readtable('ocdadult_case-controls_SubVol_noanxiety.csv');
summary_stats.SubVol_anxiety_vs_noanxiety_adult = readtable('ocdadult_anxiety-noanxiety_SubVol.csv');

summary_stats.SubVol_case_vs_controls_pediatric = readtable('ocdpediatric_case-controls_SubVol.csv');
summary_stats.SubVol_medicatedcase_vs_controls_pediatric = readtable('ocdpediatric_medicatedcase-controls_SubVol.csv');
summary_stats.SubVol_unmedicatedcase_vs_controls_pediatric = readtable('ocdpediatric_unmedicatedcase-controls_SubVol.csv');
summary_stats.SubVol_medicatedcase_vs_unmedicated_pediatric = readtable('ocdpediatric_medicatedcase-unmedicatedcase_SubVol.csv');

case 'schizophrenia'
summary_stats.CortThick_case_vs_controls = readtable('scz_case-controls_CortThick.csv');
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