The scripts in this directory reproduce the analyses of the curated datasets, in almost exactly the same order that they are mentioned in the article.

These scripts were written as a record of usage of the dashboard web application, which provides the same results.

Before starting, we recommend replicating our conda environment:

conda env create -f environment.yml
conda activate spt-repl

You can run all the replication scripts in one go on the public demo API:

python run_all.py http://oncopathtk.org/api

Or you can run them from your own local instance of the application:

python run_all.py "http://127.0.0.1:8080"

substituting the argument with the address of your local API server. (See Setting up a local application instance).

• These scripts just call the web API, and so they do not require Python package spatialprofilingtoolbox.
• You can alternatively store the API host in api_host.txt and omit the command-line argument above.
• The run result is here in results.txt.

One figure is generated programmatically from published source TIFF files. To run the figure generation script, alter the command below to reference your own database configuration file and path to unzipped Moldoveanu et al dataset.

python retrieve_example_plot.py dataset_directory/ ~/.spt_db.config

This plot replication requires the installation of SPT, as it's not a script in this directory. Instead, it's a command in the spt graphs CLI that uses the configuration files stored in gnn_figure/ to reproduce the plots seen in our publication.

spt graphs plot-importance-fractions --config_path gnn_figure/melanoma_intralesional_il2.config --output_filename gnn_figure/melanoma_intralesional_il2.png
spt graphs plot-importance-fractions --config_path gnn_figure/urothelial_ici.config --output_filename gnn_figure/urothelial_ici.png