From 8fab9a59e7a8a94378b0eb9a31400b7b7ca2421c Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Tue, 25 Feb 2025 17:11:14 -0800 Subject: [PATCH] Fixup: Drop genotype_nextclade coloring since it is equivalent to minor_lineage --- phylogenetic/defaults/color_orderings.tsv | 207 ---------------------- phylogenetic/defaults/config_dengue.yaml | 10 +- phylogenetic/rules/export.smk | 15 +- 3 files changed, 10 insertions(+), 222 deletions(-) diff --git a/phylogenetic/defaults/color_orderings.tsv b/phylogenetic/defaults/color_orderings.tsv index d264350..6ce3fb5 100644 --- a/phylogenetic/defaults/color_orderings.tsv +++ b/phylogenetic/defaults/color_orderings.tsv @@ -240,215 +240,8 @@ serotype_genbank denv2 serotype_genbank denv3 serotype_genbank denv4 -genotype_nextclade DENV1/I -genotype_nextclade DENV1/II -genotype_nextclade DENV1/III -genotype_nextclade DENV1/IV -genotype_nextclade DENV1/V -genotype_nextclade DENV2/AA -genotype_nextclade DENV2/AI -genotype_nextclade DENV2/AII -genotype_nextclade DENV2/AM -genotype_nextclade DENV2/C -genotype_nextclade DENV2/S -genotype_nextclade DENV3/I -genotype_nextclade DENV3/II -genotype_nextclade DENV3/III -genotype_nextclade DENV3/IV -genotype_nextclade DENV4/I -genotype_nextclade DENV4/II -genotype_nextclade DENV4/S - ################ # Hill 2024 dataset -genotype_nextclade 1I -genotype_nextclade 1I_A -genotype_nextclade 1I_B -genotype_nextclade 1I_C -genotype_nextclade 1I_D -genotype_nextclade 1I_E -genotype_nextclade 1I_E.1 -genotype_nextclade 1I_E.1.1 -genotype_nextclade 1I_E.1.2 -genotype_nextclade 1I_E.2 -genotype_nextclade 1I_E.3 -genotype_nextclade 1I_E.4 -genotype_nextclade 1I_F -genotype_nextclade 1I_G -genotype_nextclade 1I_H -genotype_nextclade 1I_H.1 -genotype_nextclade 1I_H.2 -genotype_nextclade 1I_H.3 -genotype_nextclade 1I_J -genotype_nextclade 1I_K -genotype_nextclade 1I_K.1 -genotype_nextclade 1I_K.1.1 -genotype_nextclade 1I_K.1.2 -genotype_nextclade 1I_K.2 -genotype_nextclade 1I_K.3 -genotype_nextclade 1I_K.4 -genotype_nextclade 1I_K.5 -genotype_nextclade 1I_K.6 -genotype_nextclade 1I_K.7 -genotype_nextclade 1II -genotype_nextclade 1III -genotype_nextclade 1III_A -genotype_nextclade 1III_A.1 -genotype_nextclade 1III_A.2 -genotype_nextclade 1III_A.3 -genotype_nextclade 1III_A.4 -genotype_nextclade 1III_B -genotype_nextclade 1IV -genotype_nextclade 1IV_A -genotype_nextclade 1IV_B -genotype_nextclade 1IV_B.1 -genotype_nextclade 1IV_B.2 -genotype_nextclade 1IV_C -genotype_nextclade 1V -genotype_nextclade 1V_A -genotype_nextclade 1V_B -genotype_nextclade 1V_C -genotype_nextclade 1V_D -genotype_nextclade 1V_D.1 -genotype_nextclade 1V_D.1.1 -genotype_nextclade 1V_D.1.2 -genotype_nextclade 1V_D.2 -genotype_nextclade 1V_E -genotype_nextclade 1V_E.1 -genotype_nextclade 1V_E.2 -genotype_nextclade 1V_E.3 -genotype_nextclade 1V_E.4 -genotype_nextclade 1V_F -genotype_nextclade 1V_G -genotype_nextclade 1V_H -genotype_nextclade 1V_J -genotype_nextclade 1VII -genotype_nextclade 1VII_A -genotype_nextclade 1VII_B -genotype_nextclade 2I -genotype_nextclade 2II -genotype_nextclade 2II_A -genotype_nextclade 2II_A.1 -genotype_nextclade 2II_A.1.1 -genotype_nextclade 2II_A.1.1.1 -genotype_nextclade 2II_A.1.1.2 -genotype_nextclade 2II_A.1.2 -genotype_nextclade 2II_A.2.1 -genotype_nextclade 2II_A.2.2 -genotype_nextclade 2II_B -genotype_nextclade 2II_C -genotype_nextclade 2II_C.1 -genotype_nextclade 2II_C.2 -genotype_nextclade 2II_D -genotype_nextclade 2II_D.1 -genotype_nextclade 2II_D.1.1 -genotype_nextclade 2II_D.1.2 -genotype_nextclade 2II_D.2 -genotype_nextclade 2II_D.3 -genotype_nextclade 2II_E -genotype_nextclade 2II_E.1 -genotype_nextclade 2II_E.2 -genotype_nextclade 2II_F -genotype_nextclade 2II_F.1 -genotype_nextclade 2II_F.1.1 -genotype_nextclade 2II_F.1.1.1 -genotype_nextclade 2II_F.1.1.2 -genotype_nextclade 2II_F.1.1.3 -genotype_nextclade 2II_F.1.1.4 -genotype_nextclade 2II_F.1.1.5 -genotype_nextclade 2II_F.1.1.6 -genotype_nextclade 2II_F.1.2 -genotype_nextclade 2II_F.1.3 -genotype_nextclade 2II_F.2 -genotype_nextclade 2II_F.2.1 -genotype_nextclade 2II_F.2.2 -genotype_nextclade 2III -genotype_nextclade 2III_A -genotype_nextclade 2III_A.1 -genotype_nextclade 2III_A.2 -genotype_nextclade 2III_B -genotype_nextclade 2III_C -genotype_nextclade 2III_C.1 -genotype_nextclade 2III_C.1.1 -genotype_nextclade 2III_C.1.2 -genotype_nextclade 2III_C.2 -genotype_nextclade 2III_D -genotype_nextclade 2III_D.1 -genotype_nextclade 2III_D.1.1 -genotype_nextclade 2III_D.1.2 -genotype_nextclade 2III_D.1.3 -genotype_nextclade 2III_D.2 -genotype_nextclade 2III_D.3 -genotype_nextclade 2III_E -genotype_nextclade 2IV -genotype_nextclade 2V -genotype_nextclade 2V_A -genotype_nextclade 2V_A.1 -genotype_nextclade 2V_A.1.1 -genotype_nextclade 2V_A.1.2 -genotype_nextclade 2V_A.1.3 -genotype_nextclade 2V_A.2 -genotype_nextclade 2V_A.3 -genotype_nextclade 2V_A.4 -genotype_nextclade 2V_B -genotype_nextclade 2V_C -genotype_nextclade 2V_D -genotype_nextclade 2V_E -genotype_nextclade 2VI -genotype_nextclade 3I -genotype_nextclade 3I_A -genotype_nextclade 3I_A.1 -genotype_nextclade 3I_A.1.1 -genotype_nextclade 3I_A.1.2 -genotype_nextclade 3I_A.2 -genotype_nextclade 3I_B -genotype_nextclade 3I_C -genotype_nextclade 3II -genotype_nextclade 3II_A -genotype_nextclade 3II_A.1 -genotype_nextclade 3II_A.2 -genotype_nextclade 3II_A.3 -genotype_nextclade 3II_A.4 -genotype_nextclade 3II_A.5 -genotype_nextclade 3II_B -genotype_nextclade 3III -genotype_nextclade 3III_A -genotype_nextclade 3III_A.1 -genotype_nextclade 3III_A.2 -genotype_nextclade 3III_B -genotype_nextclade 3III_B.1 -genotype_nextclade 3III_B.2 -genotype_nextclade 3III_B.3 -genotype_nextclade 3III_B.3.1 -genotype_nextclade 3III_B.3.2 -genotype_nextclade 3III_C -genotype_nextclade 3III_C.1 -genotype_nextclade 3III_C.2 -genotype_nextclade 3III_C.2.1 -genotype_nextclade 3III_C.2.2 -genotype_nextclade 3V -genotype_nextclade 4I -genotype_nextclade 4I_A -genotype_nextclade 4I_A.1 -genotype_nextclade 4I_A.1.1 -genotype_nextclade 4I_A.1.2 -genotype_nextclade 4I_A.2 -genotype_nextclade 4I_A.3 -genotype_nextclade 4I_B -genotype_nextclade 4I_B.1 -genotype_nextclade 4I_B.2 -genotype_nextclade 4II -genotype_nextclade 4III -genotype_nextclade 4II_A -genotype_nextclade 4II_A.1 -genotype_nextclade 4II_A.2 -genotype_nextclade 4II_B -genotype_nextclade 4II_B.1 -genotype_nextclade 4II_B.1.1 -genotype_nextclade 4II_B.1.2 -genotype_nextclade 4II_B.2 -genotype_nextclade 4IV - genotype 1I genotype 1II genotype 1III diff --git a/phylogenetic/defaults/config_dengue.yaml b/phylogenetic/defaults/config_dengue.yaml index 6fdffe0..f41dd9d 100644 --- a/phylogenetic/defaults/config_dengue.yaml +++ b/phylogenetic/defaults/config_dengue.yaml @@ -19,11 +19,11 @@ filter: traits: sampling_bias_correction: '3' traits_columns: - all: 'region serotype_genbank genotype_nextclade' - denv1: 'country region serotype_genbank genotype_nextclade' - denv2: 'country region serotype_genbank genotype_nextclade' - denv3: 'country region serotype_genbank genotype_nextclade' - denv4: 'country region serotype_genbank genotype_nextclade' + all: 'region serotype_genbank' + denv1: 'country region serotype_genbank' + denv2: 'country region serotype_genbank' + denv3: 'country region serotype_genbank' + denv4: 'country region serotype_genbank' clades: clade_definitions: diff --git a/phylogenetic/rules/export.smk b/phylogenetic/rules/export.smk index ea67171..7862c9f 100644 --- a/phylogenetic/rules/export.smk +++ b/phylogenetic/rules/export.smk @@ -42,8 +42,8 @@ rule prepare_auspice_config: output: auspice_config="results/defaults/{gene}/auspice_config_{serotype}.json", params: - replace_clade_key=lambda wildcard: r"clade_membership" if wildcard.gene in ['genome'] else r"genotype_nextclade", - replace_clade_title=lambda wildcard: r"Serotype" if wildcard.serotype in ['all'] else r"Dengue Genotype (Nextclade)", + replace_clade_key=lambda wildcard: r"clade_membership" if wildcard.gene in ['genome'] else r"major_lineage", + replace_clade_title=lambda wildcard: r"Serotype" if wildcard.serotype in ['all'] else r"Genotype (Nextclade)", run: data = { "title": "Real-time tracking of dengue virus evolution", @@ -79,8 +79,8 @@ rule prepare_auspice_config: "type": "categorical" }, { - "key": "genotype_nextclade", - "title": "Dengue Genotype (Nextclade)", + "key": "serotype_genbank", + "title": "Serotype (Genbank metadata)", "type": "categorical" }, { @@ -97,11 +97,6 @@ rule prepare_auspice_config: "key": "minor_lineage", "title": "Minor lineage (Nextclade)", "type": "categorical" - }, - { - "key": "serotype_genbank", - "title": "Serotype (Genbank metadata)", - "type": "categorical" } ], "geo_resolutions": [ @@ -137,7 +132,7 @@ rule prepare_auspice_config: if wildcards.gene in ['genome'] and wildcards.serotype in ['all']: clade_membership_title="Serotype (Nextstrain)" else: - clade_membership_title="Dengue Genotype (Nextstrain)" + clade_membership_title="Genotype (Nextstrain)" data["colorings"].append({ "key": "clade_membership",