geo spreadmap for branch major

ktmeaton · Mar 2, 2021 · abb53af · abb53af
1 parent 858b1f9
commit abb53af
Show file tree

Hide file tree

Showing 45 changed files with 143,067 additions and 54,849 deletions.
diff --git a/auspice/plague-phylogeography_locus-coverage.json b/auspice/plague-phylogeography_locus-coverage.json
diff --git a/docs/notes/Notes_Development.md b/docs/notes/Notes_Development.md
@@ -21,3 +21,4 @@
 1. Add latvia samples to database!
 1. Maybe write a function to condense exporting.
 1. Start working on geo notebook. Add cartopy.
+1. Fix root node timetree_coord_y
diff --git a/results/auspice/nextstrain_map_1.ORI.svg b/results/auspice/nextstrain_map_1.ORI.svg
diff --git a/results/geo/geo.tsv b/results/geo/geo.tsv
diff --git a/results/geo/geo_augur.json b/results/geo/geo_augur.json
@@ -0,0 +1,39 @@
+{
+  "alignment": "../../docs/results/latest/snippy_multi/snippy-core_chromosome.snps.filter5.aln",
+  "generated_by": {
+    "program": "augur",
+    "version": "10.3.0"
+  },
+  "input_tree": "../../results/geo/geo_divtree.nwk",
+  "nodes": {
+    "GCA_000006645.1_ASM664v1_genomic": {
+      "biosample": "SAMN02604093",
+      "biosamplecomment": "KEEP: Assembly Modern Morelli 2010 Cui 2013 Keller 2019",
+      "biovar": "Medievalis",
+      "branch_length": 2.35e-08,
+      "branch_major": "2.MED",
+      "branch_major_confidence": {
+        "2.MED": 0.9999999999999999
+      },
+      "branch_major_entropy": -9.99866855976916e-13,
+      "branch_minor": "2.MED1",
+      "branch_minor_confidence": {
+        "2.MED1": 0.9999999999999999
+      },
+      "branch_minor_entropy": -9.99866855976916e-13,
+      "branch_number": "2",
+      "branch_number_confidence": {
+        "2": 0.9999999999999999
+      },
+      "branch_number_entropy": -9.99866855976916e-13,
+      "chrom_cov": 0.9547389000000001,
+      "chrom_dep": 18.878587699999997,
+      "clock_length": -0.00010794993295348831,
+      "country": "Iran",
+      "country_confidence": {
+        "Iran": 1.0
+      },
+      "country_entropy": -1.000088900581841e-12,
+      "date": "1968",
+      "datebp": "-53",
+      "geometry":
diff --git a/results/geo/geo_divtree.nexus b/results/geo/geo_divtree.nexus
diff --git a/results/geo/geo_divtree.nwk b/results/geo/geo_divtree.nwk
diff --git a/results/geo/geo_divtree.xml b/results/geo/geo_divtree.xml
diff --git a/results/geo/geo_spreadmap_0..png b/results/geo/geo_spreadmap_0..png
diff --git a/results/geo/geo_spreadmap_0.ANT.png b/results/geo/geo_spreadmap_0.ANT.png