Skip to content

Commit

Permalink
Add same MCC color scale for Auspice as plots
Browse files Browse the repository at this point in the history
  • Loading branch information
@huddlej
huddlej committed Aug 19, 2024
1 parent 5d3e9fe commit 1d0d1b3
Showing 1 changed file with 215 additions and 150 deletions.
365 changes: 215 additions & 150 deletions ha-na-nextstrain/config/auspice_config.json
View file
Original file line number Diff line number Diff line change
@@ -1,151 +1,216 @@
{
"title": "Seasonal influenza A/H3N2 phylogeny from 2016-2018",
"colorings": [
{
"key": "confidence",
"title": "Bootstrap support",
"type": "continuous"
},
{
"key": "MCC",
"title": "MCC",
"type": "categorical"
},
{
"key": "pca_concatenated_label",
"title": "HA/NA PCA cluster",
"type": "categorical"
},
{
"key": "mds_concatenated_label",
"title": "HA/NA MDS cluster",
"type": "categorical"
},
{
"key": "t-sne_concatenated_label",
"title": "HA/NA t-SNE cluster",
"type": "categorical"
},
{
"key": "umap_concatenated_label",
"title": "HA/NA UMAP cluster",
"type": "categorical"
},
{
"key": "genetic_concatenated_label",
"title": "HA/NA genetic distance cluster",
"type": "categorical"
},
{
"key": "pca_ha_label",
"title": "HA PCA cluster",
"type": "categorical"
},
{
"key": "mds_ha_label",
"title": "HA MDS cluster",
"type": "categorical"
},
{
"key": "t-sne_ha_label",
"title": "HA t-SNE cluster",
"type": "categorical"
},
{
"key": "umap_ha_label",
"title": "HA UMAP cluster",
"type": "categorical"
},
{
"key": "genetic_ha_label",
"title": "HA genetic distance cluster",
"type": "categorical"
},
{
"key": "gt",
"title": "Genotype",
"type": "categorical"
},
{
"key": "num_date",
"title": "Date",
"type": "continuous"
},
{
"key": "clade_membership",
"title": "Clade",
"type": "categorical"
},
{
"key": "pca1",
"title": "PCA1",
"type": "continuous"
},
{
"key": "pca2",
"title": "PCA2",
"type": "continuous"
},
{
"key": "mds1",
"title": "MDS1",
"type": "continuous"
},
{
"key": "mds2",
"title": "MDS2",
"type": "continuous"
},
{
"key": "mds3",
"title": "MDS3",
"type": "continuous"
},
{
"key": "tsne_x",
"title": "t-SNE 1",
"type": "continuous"
},
{
"key": "tsne_y",
"title": "t-SNE 2",
"type": "continuous"
},
{
"key": "umap_x",
"title": "UMAP 1",
"type": "continuous"
},
{
"key": "umap_y",
"title": "UMAP 2",
"type": "continuous"
}
],
"display_defaults": {
"color_by": "MCC",
"distance_measure": "div"
},
"maintainers": [
{"name": "Sravani Nanduri"},
{"name": "John Huddleston"}
],
"filters": [
"MCC",
"pca_ha_label",
"mds_ha_label",
"t-sne_ha_label",
"umap_ha_label",
"genetic_ha_label",
"pca_concatenated_label",
"mds_concatenated_label",
"t-sne_concatenated_label",
"umap_concatenated_label",
"genetic_concatenated_label",
"clade_membership"
],

"panels": [
"tree"
]
}
"title": "Seasonal influenza A/H3N2 phylogeny from 2016-2018",
"colorings": [
{
"key": "confidence",
"title": "Bootstrap support",
"type": "continuous"
},
{
"key": "MCC",
"title": "MCC",
"type": "categorical",
"scale": [
[
"MCC_0",
"#4D21AD"
],
[
"MCC_1",
"#403FC6"
],
[
"MCC_2",
"#3F63CF"
],
[
"MCC_3",
"#4783C8"
],
[
"MCC_4",
"#539BB5"
],
[
"MCC_5",
"#63AC9B"
],
[
"MCC_6",
"#77B67F"
],
[
"MCC_7",
"#8EBC66"
],
[
"MCC_8",
"#A8BD53"
],
[
"MCC_9",
"#C1BA47"
],
[
"MCC_10",
"#D6B03F"
],
[
"MCC_11",
"#E39C39"
],
[
"MCC_12",
"#E67C33"
],
[
"MCC_13",
"#E1532B"
],
[
"MCC_14",
"#DB2823"
]
]
},
{
"key": "pca_concatenated_label",
"title": "HA/NA PCA cluster",
"type": "categorical"
},
{
"key": "mds_concatenated_label",
"title": "HA/NA MDS cluster",
"type": "categorical"
},
{
"key": "t-sne_concatenated_label",
"title": "HA/NA t-SNE cluster",
"type": "categorical"
},
{
"key": "umap_concatenated_label",
"title": "HA/NA UMAP cluster",
"type": "categorical"
},
{
"key": "genetic_concatenated_label",
"title": "HA/NA genetic distance cluster",
"type": "categorical"
},
{
"key": "pca_ha_label",
"title": "HA PCA cluster",
"type": "categorical"
},
{
"key": "mds_ha_label",
"title": "HA MDS cluster",
"type": "categorical"
},
{
"key": "t-sne_ha_label",
"title": "HA t-SNE cluster",
"type": "categorical"
},
{
"key": "umap_ha_label",
"title": "HA UMAP cluster",
"type": "categorical"
},
{
"key": "genetic_ha_label",
"title": "HA genetic distance cluster",
"type": "categorical"
},
{
"key": "gt",
"title": "Genotype",
"type": "categorical"
},
{
"key": "num_date",
"title": "Date",
"type": "continuous"
},
{
"key": "clade_membership",
"title": "Clade",
"type": "categorical"
},
{
"key": "pca1",
"title": "PCA1",
"type": "continuous"
},
{
"key": "pca2",
"title": "PCA2",
"type": "continuous"
},
{
"key": "mds1",
"title": "MDS1",
"type": "continuous"
},
{
"key": "mds2",
"title": "MDS2",
"type": "continuous"
},
{
"key": "mds3",
"title": "MDS3",
"type": "continuous"
},
{
"key": "tsne_x",
"title": "t-SNE 1",
"type": "continuous"
},
{
"key": "tsne_y",
"title": "t-SNE 2",
"type": "continuous"
},
{
"key": "umap_x",
"title": "UMAP 1",
"type": "continuous"
},
{
"key": "umap_y",
"title": "UMAP 2",
"type": "continuous"
}
],
"display_defaults": {
"color_by": "MCC",
"distance_measure": "div"
},
"maintainers": [
{
"name": "Sravani Nanduri"
},
{
"name": "John Huddleston"
}
],
"filters": [
"MCC",
"pca_ha_label",
"mds_ha_label",
"t-sne_ha_label",
"umap_ha_label",
"genetic_ha_label",
"pca_concatenated_label",
"mds_concatenated_label",
"t-sne_concatenated_label",
"umap_concatenated_label",
"genetic_concatenated_label",
"clade_membership"
],
"panels": [
"tree"
]
}

0 comments on commit 1d0d1b3

Please sign in to comment.