This is a set of scripts to use with the Pediatric Imaging, Neurocognition, and Genetics (PING) study. Please see http://pingstudy.ucsd.edu/ for more information about this study.
All installation dependencies are defined in the requirements.txt
file.
Installation steps:
git clone [email protected]:guruucsd/PING.git
cd PING
sudo pip install -r requirements.txt
If this fails:- Make sure you have pip installed: https://pip.pypa.io/en/latest/installing.html
- If it fails installing numpy or scipy, I suggest installing miniconda and installing them via
conda install numpy scipy pip
- Visit https://ping-dataportal.ucsd.edu/applications/User/requestLogin.php and request access to the PING data portal.
The following functions of the data portal are available through this scripting interface:
export.py
- Compute some derived measures from the PING data, and export to a local CSVgrouping.py
- Plot regressions, separating data by the chosen groupings.gwas.py
- PRELIMINARY--you must request access before using! download GWAS results, or launch a new GWAS study.scatter.py
- Show scatter plots, filtering columns by prefix and choosing computations for x, y, and point size.similarity.py
- Script interface for viewing similarity matrices between different PING measures. Select measures by prefix, and use correlation or partial correlation.snps.py
- Script interface for the SNP browser; find genes associated with SNPs, SNPs associated with genes, and download user data for specific genes. NOTE: PING limits SNP downloads to 5000, so use them wisely!upload.py
- Upload your local CSV with derived measures to the PING data portal, so you can access in the Data browser.
Scripts must be run with a valid username and password to the PING portal--if you don't have one, you'll need to request one.
There are two ways to pass your username and password to the scripts:
- Via the command-line: use parameters
--username=[USERNAME] --password=[PASSWORD]
- Via the shell: set the following environment variables:
PING_USERNAME
- your PING data portal username (not your email address).PING_PASSWORD
- your PING data portal password
These examples assume that you've set your username and password via shell environment variables. If you haven't, you'll need to add the --username=[USERNAME]
and --password=[PASSWORD]
options to the commands below.
python export.py
- exports data sheet, including computed measures, to a local CSV file.python grouping.py MRI_cort_area.ctx Gender
- show linear regression for each cortical area measure, with regression by gender overlaid on the same plot.python scatter.py MRI_cort_area AI:mean AI:std LH_PLUS_RH:mean
- show a scatter plot over cortical area measures, of asymmetry index mean vs. standard deviation, with dot size given by the total area (LH+RH)python similarity.py MRI_cort_area partial-correlation "Left Hemisphere"
- show a similarity matrix between all measures with the MRI_cort_area prefix, using partial correlation, for the left hemisphere only.python snps.py view STK31
- show all SNPs associated with gene STK31, according to the PING genetics DB.