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 # ATLASx Analysis tools 
 
 The data and scripts contained in this repository allow the user to reproduce the 
 Figure 3: "Pathway search comparison to dataset of pathways extracted from MetaCyc" 
-of the ATLASx manuscript from the original data files and the Supplementary Figure S3: 
-"Distribution of the length (i.e., number of reaction steps) of reconstructed MetaCyc pathways."
+of the ATLASx manuscript from the original data files and the Supplementary Figures S3 and S4: 
+"Pathway search comparison to dataset of pathways extracted from MetaCyc for 
+BNICE.ch-curated reactions" and "Distribution of the length (i.e., number of reaction steps) 
+of reconstructed MetaCyc pathways."
 
 ## Usage
 
 ### MetaCyc pathway coverage plot
 
-`$ cd NetworkAnalysis/Source`
+`$ cd MetaCycPWanalysis`
 
-Plot number of pathways covered within top-100, beyond top-100 and covered with alternative routes
+Perform the pathway search for MetaCyc, MetaCyc BNICE-curated, ATLASx and ATLASx BNICE-curated
+(running time: 5 min for edges coverage, approx. 2.5 days on 10 cores for pathway search)
 
-`$ python3 plot.py
+`$ python3 check_coverage_and_rank_pathways.py`
 
-Running this script will produce 3 plot files within the "plots" folder. 
-onlyBNICEvsAllATLASx.png - figure 3 of the manuscript
-plotGoldenDatasetPathwayLengthDistributionAll_all.png - main part of the Supplementary Figure 3
-plotGoldenDatasetPathwayLengthDistributionAll_crop.png - cropped in part of the Supplementary Figure 3
+Running this script will produce 5 output files within the output folder:
+# networkEdgesCoverage.csv
+# pw_ranking_chemATLAS_hp.csv
+# pw_ranking_chemATLAS.csv
+# pw_ranking_MetaCyc_hp.csv
+# pw_ranking_MetaCyc.csv
+
+As the script takes long time to be executed we recommend to use the existing files 
+that are stored in "output_generated_for_article" folder for plotting (copy them to output folder):
+
+To generate the plots run:
+
+`$ python3 plot_edges_coverage.py`
+
+`$ python3 plot_pathway_rank.py`
+
+The 2 scripts will generate the  figures used in the publication within the "plots" folder:
+MetaCycVsATLASx.png - figure 3A of the manuscript
+MetaCycVsATLASxBNICE.png - Supplementary Figure 3A
+pathways_rank_chemATLAS_hp.png  - figure 3B of the manuscript
+pathways_rank_chemATLAS.png - Supplementary Figure 3B
+pathways_rank_MetaCyc_hp.png  - figure 3B of the manuscript
+pathways_rank_MetaCyc.png - Supplementary Figure 3B
+plotMetacycPathwayLengthDistributionAll_all.png - main part of the Supplementary Figure 4
+plotMetacycPathwayLengthDistributionAll_crop.png - cropped in part of the Supplementary Figure 4