src README

src/README.md

@@ -8,15 +8,12 @@ The `data_processing` section focuses on processing the published data from Lasr
 
 
 ### 2. method_comparison
-METHOD COMPARISON IS DONE ON THE XXX DATASET. ->  SAY ON WHAT DATASET THE COMPARISON OF THE COMMUNICATION RESULTS WAS DONE AND ON WHAT DATASET THE RESURCE USAGE WAS DONE.
+The `method_comparison` section is divided into four parts:
 
-The `method_comparison` section is divided into three parts:
-IT SHOULD HAVE THE FOLLOWING STRUCUTRE:
 - **compare_databases:** Here, we explore and compare the original ligand-receptor databases as provided by each cell communication tool. The objective is to assess the variance between the databases and shared characteristics. 
 - **compare_algorithms:** This directory is systemetically arranged into sub-dirs of each tool:
     * **run_run_NicheNet:** Contains the process of creating a standarized ligand-receptor database, derived from the `community` database, which is then used to analyze cell communication with NicheNet
     * **run_CellPhoneDB:** Foloows the same procedure as run_NicheNet, tailored for CellPhoneDB
     * **run_community**: running the community on the datasets. 
-
-THE COMPARE RESULTS directory includes notebooks for visualizing and analyzing the output of each tool. 
-
+- **compare_results:** We used Lasry dataset for comparing the cell communication results generated by the tools. This directory includes notebooks for visualizing and analysizing the output of each tool.
+- **resource_usage:** to assess the scabiity and efficiency of the tools, we employ three distinct datasets: Lasry, Smillie, and an integrated VanGalen-Oetjen dataset. The evaluation involves subsampling these three datasets across a a range from 6 to 32 samples. This approach allows us to test how well each tool adapts to different data sizes and complexitities.