Update design variable names

Author: ahmig

config/design_plots.R

@@ -26,7 +26,7 @@ theme_update(
 )
 
 # Gene palette
-gene_colors <- c(
+GENE_PALETTE <- c(
   M = "#B4D4B4",
   N = "#B7B7B8",
   orf1ab = "#9CC4DC",
@@ -48,26 +48,26 @@ DIVERSITY_PALETTE <- c(
 )
 
 # M-L tree colors and labels
-tree_colors <- c(
+TREE_PALETTE <- c(
   tip_label = "#D944AA99",
   boot_alrt_pass = "#64ACEEB2"
 )
 
-node.size <- c(
+TREE_NODE_SIZE <- c(
   tip_label = 2,
   boot_alrt_pass = 0.8
 )
 
 # Nucleotide variants classification colors and labels
-NV_colors <- c(
+NV_TYPE_PALETTE <- c(
   Frameshift = "#568D63",
   "In frame" = "black",
   Intergenic = "#B27CF9",
   No = "#AE584A",
   Yes = "#0248FD"
 )
 
-NV_names <- c(
+NV_TYPE_NAMES <- c(
   Frameshift = "Frameshift",
   "In frame" = "Inframe",
   Intergenic = "Intergenic",
@@ -76,17 +76,17 @@ NV_names <- c(
 )
 
 # dn ds colors and labels
-dnds.labels <- c(
+DNDS_LABELS <- c(
   dn = "dN",
   ds = "dS"
 )
 
-dnds.colors <- c(
+DNDS_COLORS <- c(
   dn = "#E53E47",
   ds = "#2C47F5"
 )
 
-dnds.shapes <- c(
+DNDS_SHAPES <- c(
   dn = 2,
   ds = 4
 )

workflow/scripts/report/NV_description.R

@@ -189,11 +189,11 @@ variants <- vcf %>%
     inherit.aes = FALSE,
     width = 0.3
   ) +
-  scale_fill_manual(values = gene_colors) +
+  scale_fill_manual(values = GENE_PALETTE) +
   xlim(c(0, 29903)) +
   scale_color_manual(
-    labels = NV_names,
-    values = NV_colors
+    labels = NV_TYPE_NAMES,
+    values = NV_TYPE_PALETTE
   ) +
   scale_y_discrete(drop = FALSE) +
   labs(
@@ -227,7 +227,7 @@ window_plot <- window %>%
     limits = c(0, max(window$fractions) + 0.005)
   ) +
   xlim(c(0, 29903)) +
-  scale_color_manual(values = gene_colors) +
+  scale_color_manual(values = GENE_PALETTE) +
   labs(
     y = "Proportion of \n sites with NV",
     x = "",
@@ -312,7 +312,7 @@ window_plot_spike <- window %>%
   ) +
   xlim(c(min(spike_pos), max(spike_pos))) +
   scale_color_manual(
-    values = gene_colors,
+    values = GENE_PALETTE,
     guide = "none"
   ) +
   labs(
@@ -337,8 +337,8 @@ variants_spike <- vcf_spike %>%
   geom_point(size = 3) +
   xlim(c(min(spike_pos), max(spike_pos))) +
   scale_color_manual(
-    labels = NV_names,
-    values = NV_colors
+    labels = NV_TYPE_NAMES,
+    values = NV_TYPE_PALETTE
   ) +
   scale_y_discrete(drop = FALSE) +
   labs(

workflow/scripts/report/evo_plots.R

@@ -82,13 +82,13 @@ plot <- plot_df %>%
   geom_line() +
   scale_color_manual(
     name = "Parameter",
-    labels = dnds.labels,
-    values = dnds.colors
+    labels = DNDS_LABELS,
+    values = DNDS_COLORS
   ) +
   scale_shape_manual(
     name = "Parameter",
-    values = dnds.shapes,
-    labels = dnds.labels
+    values = DNDS_SHAPES,
+    labels = DNDS_LABELS
   ) +
   labs(
     y = "Substitution rate",

workflow/scripts/report/phylo_plots.R

@@ -242,11 +242,11 @@ p <- ggtree(tree_ml, layout = "circular") %<+% ml.tree.annot +
   geom_rootedge(0.05 * tree_ml.max.tip.length) +
   xlim(-tree_ml.max.tip.length / 3, NA) +
   scale_color_manual(
-    values = setNames(tree_colors[names(legend.names)], legend.names),
+    values = setNames(TREE_PALETTE[names(legend.names)], legend.names),
     na.translate = FALSE
   ) +
   scale_size_manual(
-    values = setNames(node.size[names(legend.names)], legend.names),
+    values = setNames(TREE_NODE_SIZE[names(legend.names)], legend.names),
     na.translate = FALSE
   )