From 39ead4112584e5894664d9bd5c0bd8772f3a7022 Mon Sep 17 00:00:00 2001
From: Ben Kaehler <5283007+BenKaehler@users.noreply.github.com>
Date: Sun, 14 Jul 2024 10:50:30 +1000
Subject: [PATCH] Closes #92

---
 q2_makarsa/_visualisation.py    |  2 +-
 q2_makarsa/tests/data/spec.json | 70 ++++++++++++++++-----------------
 2 files changed, 36 insertions(+), 36 deletions(-)

diff --git a/q2_makarsa/_visualisation.py b/q2_makarsa/_visualisation.py
index 274582c..446f6f3 100644
--- a/q2_makarsa/_visualisation.py
+++ b/q2_makarsa/_visualisation.py
@@ -166,7 +166,7 @@ def add_mv_distances(network, idx, nodes, links):
     for a in nodes:
         for b in nodes:
             d = distances[rev_idx[a["index"]]][rev_idx[b["index"]]]
-            b[str(a["index"])] = d
+            b[str(a["index"])] = max(1, d)
             radius = max(radius, d)
         for link in links:
             link[str(a["index"])] = max(
diff --git a/q2_makarsa/tests/data/spec.json b/q2_makarsa/tests/data/spec.json
index 49da0d0..3d1eb09 100644
--- a/q2_makarsa/tests/data/spec.json
+++ b/q2_makarsa/tests/data/spec.json
@@ -191,7 +191,7 @@
     {
      "index": 0,
      "Feature": "HKcs0",
-     "0": 0,
+     "0": 1,
      "1": 4,
      "2": 4,
      "3": 4,
@@ -231,7 +231,7 @@
      "index": 1,
      "Feature": "bPSEb",
      "0": 4,
-     "1": 0,
+     "1": 1,
      "2": 2,
      "3": 2,
      "4": 2,
@@ -271,7 +271,7 @@
      "Feature": "X3KD3L",
      "0": 4,
      "1": 2,
-     "2": 0,
+     "2": 1,
      "3": 4,
      "4": 3,
      "5": 3,
@@ -311,7 +311,7 @@
      "0": 4,
      "1": 2,
      "2": 4,
-     "3": 0,
+     "3": 1,
      "4": 2,
      "5": 3,
      "6": 3,
@@ -351,7 +351,7 @@
      "1": 2,
      "2": 3,
      "3": 2,
-     "4": 0,
+     "4": 1,
      "5": 3,
      "6": 2,
      "7": 2,
@@ -391,7 +391,7 @@
      "2": 3,
      "3": 3,
      "4": 3,
-     "5": 0,
+     "5": 1,
      "6": 3,
      "7": 4,
      "8": 3,
@@ -431,7 +431,7 @@
      "3": 3,
      "4": 2,
      "5": 3,
-     "6": 0,
+     "6": 1,
      "7": 3,
      "8": 4,
      "9": 2,
@@ -471,7 +471,7 @@
      "4": 2,
      "5": 4,
      "6": 3,
-     "7": 0,
+     "7": 1,
      "8": 5,
      "9": 2,
      "10": 1,
@@ -511,7 +511,7 @@
      "5": 3,
      "6": 4,
      "7": 5,
-     "8": 0,
+     "8": 1,
      "9": 4,
      "10": 6,
      "11": 4,
@@ -551,7 +551,7 @@
      "6": 2,
      "7": 2,
      "8": 4,
-     "9": 0,
+     "9": 1,
      "10": 3,
      "11": 2,
      "12": 1,
@@ -591,7 +591,7 @@
      "7": 1,
      "8": 6,
      "9": 3,
-     "10": 0,
+     "10": 1,
      "11": 5,
      "12": 4,
      "13": 6,
@@ -631,7 +631,7 @@
      "8": 4,
      "9": 2,
      "10": 5,
-     "11": 0,
+     "11": 1,
      "12": 3,
      "13": 5,
      "14": 2,
@@ -671,7 +671,7 @@
      "9": 1,
      "10": 4,
      "11": 3,
-     "12": 0,
+     "12": 1,
      "13": 4,
      "14": 2,
      "15": 1,
@@ -711,7 +711,7 @@
      "10": 6,
      "11": 5,
      "12": 4,
-     "13": 0,
+     "13": 1,
      "14": 4,
      "15": 3,
      "16": 4,
@@ -751,7 +751,7 @@
      "11": 2,
      "12": 2,
      "13": 4,
-     "14": 0,
+     "14": 1,
      "15": 2,
      "16": 2,
      "17": 3,
@@ -791,7 +791,7 @@
      "12": 1,
      "13": 3,
      "14": 2,
-     "15": 0,
+     "15": 1,
      "16": 2,
      "17": 2,
      "18": 3,
@@ -831,7 +831,7 @@
      "13": 4,
      "14": 2,
      "15": 2,
-     "16": 0,
+     "16": 1,
      "17": 3,
      "18": 5,
      "19": 6,
@@ -871,7 +871,7 @@
      "14": 3,
      "15": 2,
      "16": 3,
-     "17": 0,
+     "17": 1,
      "18": 3,
      "19": 4,
      "20": 3,
@@ -911,7 +911,7 @@
      "15": 3,
      "16": 5,
      "17": 3,
-     "18": 0,
+     "18": 1,
      "19": 2,
      "20": 5,
      "21": 5,
@@ -951,7 +951,7 @@
      "16": 6,
      "17": 4,
      "18": 2,
-     "19": 0,
+     "19": 1,
      "20": 6,
      "21": 6,
      "22": 5,
@@ -991,7 +991,7 @@
      "17": 3,
      "18": 5,
      "19": 6,
-     "20": 0,
+     "20": 1,
      "21": 1,
      "22": 1,
      "23": 2,
@@ -1031,7 +1031,7 @@
      "18": 5,
      "19": 6,
      "20": 1,
-     "21": 0,
+     "21": 1,
      "22": 2,
      "23": 2,
      "24": 2,
@@ -1071,7 +1071,7 @@
      "19": 5,
      "20": 1,
      "21": 2,
-     "22": 0,
+     "22": 1,
      "23": 1,
      "24": 2,
      "25": 2,
@@ -1111,7 +1111,7 @@
      "20": 2,
      "21": 2,
      "22": 1,
-     "23": 0,
+     "23": 1,
      "24": 2,
      "25": 2,
      "26": 1,
@@ -1151,7 +1151,7 @@
      "21": 2,
      "22": 2,
      "23": 2,
-     "24": 0,
+     "24": 1,
      "25": 2,
      "26": 1,
      "27": 2,
@@ -1191,7 +1191,7 @@
      "22": 2,
      "23": 2,
      "24": 2,
-     "25": 0,
+     "25": 1,
      "26": 1,
      "27": 1,
      "28": 1,
@@ -1231,7 +1231,7 @@
      "23": 1,
      "24": 1,
      "25": 1,
-     "26": 0,
+     "26": 1,
      "27": 1,
      "28": 1,
      "29": 2,
@@ -1271,7 +1271,7 @@
      "24": 2,
      "25": 1,
      "26": 1,
-     "27": 0,
+     "27": 1,
      "28": 1,
      "29": 1,
      "30": 3,
@@ -1311,7 +1311,7 @@
      "25": 1,
      "26": 1,
      "27": 1,
-     "28": 0,
+     "28": 1,
      "29": 2,
      "30": 3,
      "31": 4,
@@ -1351,7 +1351,7 @@
      "26": 2,
      "27": 1,
      "28": 2,
-     "29": 0,
+     "29": 1,
      "30": 4,
      "31": 2,
      "32": 2,
@@ -1391,7 +1391,7 @@
      "27": 3,
      "28": 3,
      "29": 4,
-     "30": 0,
+     "30": 1,
      "31": 6,
      "32": 3,
      "33": 3,
@@ -1431,7 +1431,7 @@
      "28": 4,
      "29": 2,
      "30": 6,
-     "31": 0,
+     "31": 1,
      "32": 4,
      "33": 5,
      "34": 6
@@ -1471,7 +1471,7 @@
      "29": 2,
      "30": 3,
      "31": 4,
-     "32": 0,
+     "32": 1,
      "33": 1,
      "34": 2
     },
@@ -1511,7 +1511,7 @@
      "30": 3,
      "31": 5,
      "32": 1,
-     "33": 0,
+     "33": 1,
      "34": 3
     },
     {
@@ -1551,7 +1551,7 @@
      "31": 6,
      "32": 2,
      "33": 3,
-     "34": 0
+     "34": 1
     }
    ]
   },