first geo attempt spreadmap for branch number

ktmeaton · Mar 2, 2021 · 858b1f9 · 858b1f9
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diff --git a/results/geo/geo_spreadmap_0..png b/results/geo/geo_spreadmap_0..png
diff --git a/results/geo/geo_spreadmap_0.PRE.png b/results/geo/geo_spreadmap_0.PRE.png
diff --git a/results/geo/geo_spreadmap_0.PRE.svg b/results/geo/geo_spreadmap_0.PRE.svg
diff --git a/results/geo/geo_spreadmap_0.svg b/results/geo/geo_spreadmap_0.svg
diff --git a/results/geo/geo_spreadmap_1..png b/results/geo/geo_spreadmap_1..png
diff --git a/results/geo/geo_spreadmap_1.ANT.png b/results/geo/geo_spreadmap_1.ANT.png
diff --git a/results/geo/geo_spreadmap_1.ANT.svg b/results/geo/geo_spreadmap_1.ANT.svg
diff --git a/results/geo/geo_spreadmap_1.PRE.png b/results/geo/geo_spreadmap_1.PRE.png
diff --git a/results/geo/geo_spreadmap_1.PRE.svg b/results/geo/geo_spreadmap_1.PRE.svg
diff --git a/results/geo/geo_spreadmap_1.svg b/results/geo/geo_spreadmap_1.svg
diff --git a/results/geo/geo_spreadmap_2..png b/results/geo/geo_spreadmap_2..png
diff --git a/results/geo/geo_spreadmap_2.svg b/results/geo/geo_spreadmap_2.svg
diff --git a/results/geo/geo_spreadmap_3..png b/results/geo/geo_spreadmap_3..png
diff --git a/results/geo/geo_spreadmap_3.svg b/results/geo/geo_spreadmap_3.svg
diff --git a/results/geo/geo_spreadmap_4..png b/results/geo/geo_spreadmap_4..png
diff --git a/results/geo/geo_spreadmap_4.ANT.png b/results/geo/geo_spreadmap_4.ANT.png
diff --git a/results/geo/geo_spreadmap_4.ANT.svg b/results/geo/geo_spreadmap_4.ANT.svg
diff --git a/results/geo/geo_spreadmap_4.svg b/results/geo/geo_spreadmap_4.svg
diff --git a/workflow/notebooks/4_locus_coverage.py.ipynb b/workflow/notebooks/4_locus_coverage.py.ipynb
@@ -68,14 +68,13 @@
     "aln_path = \"../../docs/results/latest/snippy_multi/snippy-core_chromosome.snps.filter5.aln\"\n",
     "locus_df_path = \"../../results/locus_coverage/all/locus_coverage.txt\"\n",
     "\n",
-    "\n",
+    "# Auspice\n",
     "auspice_latlon_path = \"../../results/parse_tree/parse_tree_latlon.tsv\"\n",
     "auspice_colors_path = \"../../results/parse_tree/parse_tree_colors.tsv\"\n",
-    "\n",
-    "# static dir\n",
     "auspice_config_path = \"../../config/auspice_config.json\"\n",
     "auspice_remote_dir_path = \"../../auspice/\"\n",
     "\n",
+    "# Output\n",
     "outdir = \"../../results/locus_coverage/all/\"\n",
     "\n",
     "# Create output directory if it doesn't exist\n",
@@ -4824,7 +4823,7 @@
    "id": "smart-string",
    "metadata": {},
    "source": [
-    "## Augur JSON"
+    "## Auspice JSON"
    ]
   },
   {