From 3756257c9d4f0146ab7cc1c32f7efde26bf4269b Mon Sep 17 00:00:00 2001
From: vhu43 <67619615+vhu43@users.noreply.github.com>
Date: Mon, 3 Jul 2023 16:30:56 -0700
Subject: [PATCH] Update SequenceAnalyzer.py

Set distance to hamming.
---
 rules/utils/SequenceAnalyzer.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/rules/utils/SequenceAnalyzer.py b/rules/utils/SequenceAnalyzer.py
index 6661896..9839f31 100644
--- a/rules/utils/SequenceAnalyzer.py
+++ b/rules/utils/SequenceAnalyzer.py
@@ -602,7 +602,7 @@ def dimension_reduction(self, NTorAA, idx=None, onehot=True, encoding=None, dime
             matrix = matrix[:, different_values]
             
         # initializing the pacmap instance
-        embedding = pm.PaCMAP(n_components=dimensions, MN_ratio=0.5, FP_ratio=2.0)
+        embedding = pm.PaCMAP(n_components=dimensions, MN_ratio=0.5, FP_ratio=2.0, distance="hamming")
 
         # fit the data to provided number of dimensions then make into a dataframe with # of columns = dimensions
         reduced = embedding.fit_transform(matrix, init="pca")
@@ -729,4 +729,4 @@ def genotype_modify(self, substitutions, deletions):
                 integer[posi:posi+number] = self.encoder_dict['-']
         
         return integer
-    
\ No newline at end of file
+