Update AF trajectory panel and legend labels

Author: ahmig

workflow/rules/report.smk

@@ -277,6 +277,9 @@ rule af_trajectory_panel_plot:
     conda: "../envs/renv.yaml"
     params:
         design = config["PLOTS"],
+        n_plot_columns = 3,
+        plot_row_height_mm = 35,
+        plot_width_mm = 159.2,
         random_color_seed = 7291,
     input:
         fmt_variants = OUTDIR/f"{OUTPUT_NAME}.variants.filled.dated.tsv",

workflow/scripts/report/af_trajectory_panel_plot.R

@@ -21,48 +21,52 @@ log_info("Reading subset of variants to represent")
 selected.variants <- read_lines(snakemake@input$subset)
 
 # Set plot height depending on the number of SNPs assuming 4 columns in the plot
-log_debug("Calculating plot height")
-plot.height <- ceiling(length(selected.variants) / 4) * 42
+plot.rows <- ceiling(
+  length(selected.variants) / snakemake@params$n_plot_columns
+)
+plot.height <- max(100, plot.rows * snakemake@params$plot_row_height_mm)
+log_debug("Setting total plot height to {plot.height} mm with {plot.rows} rows")
 
 log_info("Plotting {length(selected.variants)} SNPs allele frequency trajectories in time")
 selected.colors <- sample(TRAJECTORY.PANEL.COLORS, length(selected.variants))
 log_debug("Selected color: {selected.colors}")
 p <- variants %>%
   filter(VARIANT_NAME %in% selected.variants) %>%
+  mutate(gPOS = reorder(paste0("g.", POS), POS)) %>%
   ggplot() +
   aes(
     x = interval,
     y = ALT_FREQ,
-    color = VARIANT_NAME
+    color = reorder(glue::glue("{gPOS}\n{VARIANT_NAME}"), POS)
   ) +
   scale_color_manual(values = selected.colors) +
   geom_point() +
   geom_line() +
   theme(
     legend.position = "bottom",
-    legend.text = element_text(size = 9)
+    legend.text = element_text(size = 9),
+    legend.title = element_blank(),
+    legend.spacing.y = unit(3, "mm")
   ) +
   labs(
     x = "Days since first sample",
-    y = "Frequency",
-    color = "NV"
+    y = "Frequency"
   ) +
   guides(color = guide_legend(ncol = 3))
 
 if (length(selected.variants) > 1) {
   p <- p +
     facet_wrap(
-      vars(POS),
-      nrow = ceiling(length(selected.variants) / 4),
-      ncol = 4
+      vars(gPOS),
+      ncol = snakemake@params$n_plot_columns
     )
 }
 
 ggsave(
   filename = snakemake@output[["plot"]],
   plot = p,
-  width = 159.2,
-  height = max(100, plot.height),
+  width = snakemake@params$plot_width_mm,
+  height = plot.height,
   units = "mm",
   dpi = 250
 )