new geo stats

workflow/notebooks/functions.py

@@ -538,3 +538,22 @@ def calc_peak_ci(data, confidence, tails):
 def func_exp(x, a, b, c):
     """Fit an exponential function."""
     return a * x + b * x ** 2 + c
+
+# Find the closest relative
+def closest_terminal_node(sample, tree):
+    """Return the closests terminal node to the sample in tree."""
+    sample1 = sample
+    closest_dist = 999
+    closest_sample = None
+
+    # Search through tree and calculate genetic distances
+    for sample2 in tree.get_terminals():
+        # Skip self
+        if sample1 == sample2: continue
+
+        gene_dist = tree.distance(sample1, sample2)
+        if gene_dist < closest_dist:
+            closest_dist = gene_dist
+            closest_sample = sample2
+
+    return closest_sample

workflow/scripts/screenshot.py

@@ -33,16 +33,20 @@
 url = project + query
 output = "{}_{}_{}.pdf".format(clade, panel, color)
 
-url = "https://nextstrain.org/community/ktmeaton/plague-phylogeography-projects@main/main/ml/all?d=map&f_population=1.PRE,2.MED,0.PE&legend=closed&onlyPanels&p=full&sidebar=closed&transmissions=hide"
-output = "map_caucasus.pdf"
+url ="https://nextstrain.org/community/ktmeaton/plague-phylogeography-projects@main/main/ml/1.IN?branchLabel=Province%20Confidence&c=province&d=map&legend=closed&m=div&onlyPanels&p=full&sidebar=closed&tl=host_order_raw&transmissions=hide"
+output = "map_divtree.pdf"
+
+
 
 
 print(url)
 print()
 
 wait = 10
-width = 1920
-height = 1080
+#width = 1920
+#height = 1080
+width = 720
+height = 540
 options = {
     "path": output,
     "format": "A0",