spDDB’s Domain Detection evaluation metrics - DLPFC 151508

!git clone https://github.com/Zafar-Lab/spDDB.git
%cd spDDB/Experiments/_Domain_Detection_Metrics_Calculation/

fatal: destination path 'spDDB' already exists and is not an empty directory.
/content/spDDB/Experiments/_Domain_Detection_Metrics_Calculation

!pip install scanpy
!pip install squidpy

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from Metrics import *

from google.colab import drive
drive.mount('/content/drive')

Drive already mounted at /content/drive; to attempt to forcibly remount, call drive.mount("/content/drive", force_remount=True).

dataset_dict = {"DLPFC151508":{
                "st_path": f"/content/drive/MyDrive/Benchmarking_Shared/spDDB_tutorials/1_data/ST.h5ad",
                "gnd_path": f"/content/drive/MyDrive/Benchmarking_Shared/spDDB_tutorials/1_data/metadata.tsv"}
            }
method_dict = {"DLPFC151508":{"SCANIT":"/content/drive/MyDrive/Benchmarking_Shared/spDDB_tutorials/7_data/151508/output_SCANIT_151508.csv"}}

'''
output is a new csv file of all methods and datasets for each metric, with the queried values populated.
Old files of the same name will be overwritten.
To compute for multiple methods and datasets, each new method and dataset can be added in the below dictionaries and queried in the function.
'''
output_path = "/content/drive/MyDrive/Benchmarking_Shared/spDDB_tutorials/7_data/outputs"
compute_metrics(["DLPFC151508"], dataset_dict, ["SCANIT"], method_dict, error_log_file= output_path + "error_log.txt", output_dir= output_path, metric_names="all")

saving to /content/drive/MyDrive/Benchmarking_Shared/spDDB_tutorials/7_data/outputs

/usr/local/lib/python3.12/dist-packages/anndata/_core/anndata.py:1884: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.
  utils.warn_names_duplicates("var")

Running on DLPFC151508_SCANIT
Saved ARI results to /content/drive/MyDrive/Benchmarking_Shared/spDDB_tutorials/7_data/outputs/ARI_results.csv
Saved NMI results to /content/drive/MyDrive/Benchmarking_Shared/spDDB_tutorials/7_data/outputs/NMI_results.csv
Saved CHAOS results to /content/drive/MyDrive/Benchmarking_Shared/spDDB_tutorials/7_data/outputs/CHAOS_results.csv
Saved PAS results to /content/drive/MyDrive/Benchmarking_Shared/spDDB_tutorials/7_data/outputs/PAS_results.csv
Saved ASW results to /content/drive/MyDrive/Benchmarking_Shared/spDDB_tutorials/7_data/outputs/ASW_results.csv
Saved HOM results to /content/drive/MyDrive/Benchmarking_Shared/spDDB_tutorials/7_data/outputs/HOM_results.csv
Saved COM results to /content/drive/MyDrive/Benchmarking_Shared/spDDB_tutorials/7_data/outputs/COM_results.csv

'''
This function is used to update values in the previously created metrics csv files for new methods and datasets.
'''
update_metrics(["DLPFC151508"], dataset_dict,["SCANIT"], method_dict, error_log_file= output_path + "error_log.txt", output_dir= output_path, metric_names="all")

Saved ARI results to /content/drive/MyDrive/Benchmarking_Shared/spDDB_tutorials/7_data/outputs/ARI_results.csv
Saved NMI results to /content/drive/MyDrive/Benchmarking_Shared/spDDB_tutorials/7_data/outputs/NMI_results.csv
Saved CHAOS results to /content/drive/MyDrive/Benchmarking_Shared/spDDB_tutorials/7_data/outputs/CHAOS_results.csv
Saved PAS results to /content/drive/MyDrive/Benchmarking_Shared/spDDB_tutorials/7_data/outputs/PAS_results.csv
Saved ASW results to /content/drive/MyDrive/Benchmarking_Shared/spDDB_tutorials/7_data/outputs/ASW_results.csv
Saved HOM results to /content/drive/MyDrive/Benchmarking_Shared/spDDB_tutorials/7_data/outputs/HOM_results.csv
Saved COM results to /content/drive/MyDrive/Benchmarking_Shared/spDDB_tutorials/7_data/outputs/COM_results.csv