update analysis_replication for gnn plots

analysis_replication/README.md

@@ -30,11 +30,20 @@ substituting the argument with the address of your local API server. (See *Setti
 - 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](results.txt).
 
-# Cell arrangment figure generation
+## Cell arrangement figure generation
 
 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.
 
 ```bash
 python retrieve_example_plot.py dataset_directory/ ~/.spt_db.config
 ```
+
+## GNN importance fractions figure generation
+
+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.
+
+```bash
+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
+```

analysis_replication/gnn_figure/melanoma_intralesional_il2.config

@@ -0,0 +1,15 @@
+[general]
+study_name = Melanoma intralesional IL2
+
+[plot-importance-fractions]
+host_name = http://oncopathtk.org/api
+phenotypes = Tumor, Adipocyte or Langerhans cell, Natural killer cell, CD4+ T cell, Nerve, B cell, CD4+/CD8+ T cell, CD4+ regulatory T cell, CD8+ natural killer T cell, CD8+ regulatory T cell, CD8+ T cell, Double negative regulatory T cell, T cell/null phenotype, Natural killer T cell, CD4+ natural killer T cell
+plugins = cg-gnn, graph-transformer
+figure_size = 11, 8
+orientation = horizontal
+[plot-importance-fractions.cohort0]
+index_int = 1
+label = Non-responder
+[plot-importance-fractions.cohort1]
+index_int = 3
+label = Responder

analysis_replication/gnn_figure/urothelial_ici.config

@@ -0,0 +1,15 @@
+[general]
+study_name = Urothelial ICI
+
+[plot-importance-fractions]
+host_name = http://oncopathtk.org/api
+phenotypes = Tumor, CD4- CD8- T cell, T cytotoxic cell, T helper cell, Macrophage, intratumoral CD3+ LAG3+, Regulatory T cell
+plugins = cg-gnn, graph-transformer
+figure_size = 14, 5
+orientation = vertical
+[plot-importance-fractions.cohort0]
+index_int = 1
+label = Responder
+[plot-importance-fractions.cohort1]
+index_int = 2
+label = Non-responder