PVM Dashboard 2024-02-15

pvm-igm · Feb 15, 2024 · f12d45e · f12d45e
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commit f12d45e
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Showing 2 changed files with 93 additions and 86 deletions.
diff --git a/index.Rmd b/index.Rmd
@@ -521,7 +521,7 @@ sc2_variants <- list(
   "VOC: Omicron (FE.1)"  = c("FE.1", "FE.1.2"),
   "VOC: Omicron (GK.1)" = c("GK.1", unique(gi$pangolin_lineage[grep("^GK\\.1\\.", gi$pangolin_lineage)])),
     "VOC: Omicron (JD.1)" = c("JD.1", unique(gi$pangolin_lineage[grep("^JD\\.1\\.", gi$pangolin_lineage)])),
-  "VOC: Omicron (DL.1)" = c("DL.1", unique(gi$pangolin_lineage[grep("^DL\\.1\\.", gi$pangolin_lineage)])))
+  "VOC: Omicron (DL.1)" = c("DL.1", unique(gi$pangolin_lineage[grep("^DL\\.1\\.", gi$pangolin_lineage)])), unique(gi$pangolin_lineage[grep("^JN\\.1\\.", gi$pangolin_lineage)])))
 
 
 sc2_oms <- structure(c(rep(names(sc2_variants), sapply(sc2_variants, length))),
@@ -603,6 +603,7 @@ gi_bahia_epiwseq_plot <- plotly::ggplotly(
       "VOC: Omicron (GK.1)" = "#0000FF",
       "VOC: Omicron (FE.1)" = "#FFFF00",
       "VOC: Omicron (JD.1)" = "#FF0066",
+      "VOC: Omicron (JN.1)" = "#336600",
       "Others" = "#999999")) + theme_light() +
     theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1, size = 8),
           axis.text.y = element_text(hjust = 1, size = 8),
@@ -644,6 +645,7 @@ gi_salvador_epiwseq <- plotly::ggplotly(
       "VOC: Omicron (GK.1)" = "#0000FF",
       "VOC: Omicron (FE.1)" = "#FFFF00",
       "VOC: Omicron (JD.1)" = "#FF0066",
+      "VOC: Omicron (JN.1)" = "#336600",
       "Others" = "#999999")) + theme_light() +
     theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1, size = 8),
           axis.text.y = element_text(hjust = 1, size = 8),
@@ -685,6 +687,7 @@ gi_irece_epiwseq_plot <- plotly::ggplotly(
       "VOC: Omicron (GK.1)" = "#0000FF",
       "VOC: Omicron (FE.1)" = "#FFFF00",
       "VOC: Omicron (JD.1)" = "#FF0066",
+      "VOC: Omicron (JN.1)" = "#336600",
       "Others" = "#999999")) + theme_light() +
     theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1, size = 8),
           axis.text.y = element_text(hjust = 1, size = 8),
@@ -882,6 +885,7 @@ gi_hsr_epiwseq_plot <- plotly::ggplotly(
       "VOC: Omicron (GK.1)" = "#0000FF",
       "VOC: Omicron (FE.1)" = "#FFFF00",
       "VOC: Omicron (JD.1)" = "#FF0066",
+      "VOC: Omicron (JN.1)" = "#336600",
       "Others" = "#999999")) + theme_light() +
     theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1, size = 8),
           axis.text.y = element_text(hjust = 1, size = 8),
@@ -1048,6 +1052,7 @@ gi_labcov_epiwseq <- plotly::ggplotly(
       "VOC: Omicron (GK.1)" = "#0000FF",
       "VOC: Omicron (FE.1)" = "#FFFF00",
       "VOC: Omicron (JD.1)" = "#FF0066",
+      "VOC: Omicron (JN.1)" = "#336600",
       "Others" = "#999999")) + theme_light() +
     theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1, size = 8),
           axis.text.y = element_text(hjust = 1, size = 8),
@@ -1233,6 +1238,7 @@ gi_lacen_ba_epiwseq_plot <- plotly::ggplotly(
       "VOC: Omicron (GK.1)" = "#0000FF",
       "VOC: Omicron (FE.1)" = "#FFFF00",
       "VOC: Omicron (JD.1)" = "#FF0066",
+      "VOC: Omicron (JN.1)" = "#336600",
       "Others" = "#999999")) + theme_light() +
     theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1, size = 8),
           axis.text.y = element_text(hjust = 1, size = 8),
@@ -1399,6 +1405,7 @@ gi_ljc_epiwseq_plot <- plotly::ggplotly(
       "VOC: Omicron (GK.1)" = "#0000FF",
       "VOC: Omicron (FE.1)" = "#FFFF00",
       "VOC: Omicron (JD.1)" = "#FF0066",
+      "VOC: Omicron (JN.1)" = "#336600",
       "Others" = "#999999")) + theme_light() +
     theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1, size = 8),
           axis.text.y = element_text(hjust = 1, size = 8),