Update README.md

Author: Luissolis2020

README.md

@@ -56,9 +56,12 @@ NOTE: These are the version the program was created on, future versions of these
 5. If you want a CAM model generated for the input sequence run:
    > EnhancerMatcher.py two_similar_enhancers.fa sequences.fa --cam
 
-6. In the output folder, the generated CAM is called sequence_CAM.pdf
+6. If you want a colorblind friendly CAM model generated for the input sequence run:
+   > EnhancerMatcher.py two_similar_enhancers.fa sequences.fa --cam --colorblind
 
-   Opening it will show a heatmap for the given sequence, the dark red regions show the main area that influenced EnhancerMatcher's final decision. Please read the main paper for more details.
+7. In the output folder, the generated CAM is called sequence_CAM.pdf
+
+   Opening it will show a heatmap for the given sequence, the dark red regions show the main area that influenced EnhancerMatcher's final decision. Please read the main paper for more details. Provided is a colorblind option where in this case the yellow brigher spots are main interest spots. 
 
 If you wish to run EnhancerMatcher via the jupyter notebook:
 
@@ -74,9 +77,13 @@ If you wish to run EnhancerMatcher via the jupyter notebook:
 
     Set this parameter to output_cam_pdf = True
 
-4. If you want to change the output directory locate and edit output_dir with your output directory.
+4. If you want a colorblind friendly CAM model generated then locate the second cell and locate colorblind_friendly.
+
+    Set this parameter to colorblind_friendly = True
 
-5. Once you edit the parameters, run the entire notebook and the outputs will be generated in the output directory.
+5. If you want to change the output directory locate and edit output_dir with your output directory.
+
+6. Once you edit the parameters, run the entire notebook and the outputs will be generated in the output directory.
 
 ## To Run our Tests:
 1. Look inside the Test_Input folder, inside are two fasta files:
@@ -91,6 +98,9 @@ If you wish to run EnhancerMatcher via the jupyter notebook:
    If you want to generate a CAM output for each sequence run:
    > python EnhancerMatcher.py Test_Input/input1.fasta Test_Input/input2.fasta --cam
 
+   If you want to generate a colorblind friendly CAM output for each sequence run:
+   > python EnhancerMatcher.py Test_Input/input1.fasta Test_Input/input2.fasta --cam --colorblind
+
 3. Inside the Output folder will be the results and CAM models for each given sequence.
 
 4. If you want to use the jupyter notebook then open EnhancerMatcher.ipynb