Make some plots from junifer output for initial inspection.
pip install git+https://github.com/LeSasse/juniplot.git
Data used for these examples was obtained from the AOMIC PIOP1 dataset.
juniplot allows you to plot functional connectivity markers obtained in a
junifer pipeline. Importantly,
it works for HDF5FeatureStorage data only.
You can run juniplot on a single element_* file. Just specify the output path.
In addition you should use the --single-output flag.
Optionally you can specify a matplotlib colormap.
By default juniplot will save figures as png files, but using the --format
parameter, you can also save it as pdf or as svg.
For large datasets, png is likely the fastest, but pdf and svg of course
have the advantage, that they are scalable and therefore sharper overall.
To give it a try on some real data you can use the example provided at: https://gin.g-node.org/LeSasse/juniplot-example
git clone https://gin.g-node.org/LeSasse/juniplot-example.git
cd juniplot-example
Run for a single element:
juniplot \
aomic_piop1/element_0157_restingstate_aomic_piop1.hdf5 \
plots/single \
--cmap "coolwarm" \
--single-output
The example plot may look as follows:
You can also set the --n-jobs parameter. This will run plotting for each
marker that you defined in your junifer yaml separately. Keep in mind, that depending
on the size of your dataset, this can take some time.
juniplot will make a figure for every subject, every marker of that subject,
and then also a group average for each marker. Group averages are derived
by Fisher's r-to-z transform, then averaging, and then z-to-r transforming
back the average.
Run for the collected file:
juniplot \
aomic_piop1/aomic_piop1.hdf5 \
plots/group \
--cmap "coolwarm" \
--n-jobs 16
An example of one of the individual subjects from this one can look as follows:
An example of some group average data looks as follows:
If you want to avoid running all subjects and are only interested in the group average
plot you can also use the --average-only flag. This will then only plot the group
average matrices.
juniplot \
aomic_piop1/aomic_piop1.hdf5 \
plots/group \
--cmap "coolwarm" \
--average-only