Latest modifiactions from Nicole suggestions

R/00_text_style.R

@@ -0,0 +1,46 @@
+# Global text styling shared across every plot in this script. Applied to the
+# final patchwork via `& big_helvetica_theme()` so it cascades to every
+# sub-panel without rewriting each individual theme() call inside the
+# per-plot helpers.
+
+# big_helvetica_theme(): theme() partial that forces every text element to
+# Helvetica, plain face (no bold) and a much larger size. Override individual
+# pieces with the `base_size` argument.
+#
+# Example:
+#   p <- p_lz / p_beta
+#   p & big_helvetica_theme()           # default sizes
+#   p & big_helvetica_theme(base_size = 22)  # even larger
+big_helvetica_theme <- function(base_size = 18, family = "Helvetica") {
+  fam <- family
+  bs  <- as.numeric(base_size)
+  ggplot2::theme(
+    text          = ggplot2::element_text(family = fam, face = "plain", size = bs),
+    # Titles are LEFT-aligned (hjust = 0) so a wide title can't overflow into
+    # the adjacent column when the LocusZoom column is narrower than the
+    # others. The original ggplot default `hjust = 0.5` re-centres the title
+    # over its panel and a long title spills sideways into the next panel.
+    plot.title    = ggplot2::element_text(family = fam, face = "plain",
+                                          size = bs + 2, hjust = 0,
+                                          margin = ggplot2::margin(b = bs * 0.25)),
+    plot.subtitle = ggplot2::element_text(family = fam, face = "plain",
+                                          size = bs - 2, hjust = 0),
+    # Anchor titles to the whole plot/slot (not just the inner panel) so a
+    # multi-line title in a narrower column doesn't lean into the neighbour.
+    plot.title.position    = "plot",
+    plot.caption.position  = "plot",
+    plot.caption  = ggplot2::element_text(family = fam, face = "plain", size = bs - 4),
+    # Axis labels (titles) and tick text are bumped one step above the base
+    # size so the chromosome / Mb / -log10(P) labels read clearly even when
+    # the LocusZoom column shares width with the beta / Z panels.
+    axis.title    = ggplot2::element_text(family = fam, face = "plain", size = bs + 3),
+    axis.title.x  = ggplot2::element_text(family = fam, face = "plain", size = bs + 3),
+    axis.title.y  = ggplot2::element_text(family = fam, face = "plain", size = bs + 3),
+    axis.text     = ggplot2::element_text(family = fam, face = "plain", size = bs + 2),
+    axis.text.x   = ggplot2::element_text(family = fam, face = "plain", size = bs + 2),
+    axis.text.y   = ggplot2::element_text(family = fam, face = "plain", size = bs + 2),
+    legend.title  = ggplot2::element_text(family = fam, face = "plain", size = bs - 2),
+    legend.text   = ggplot2::element_text(family = fam, face = "plain", size = bs - 4),
+    strip.text    = ggplot2::element_text(family = fam, face = "plain", size = bs)
+  )
+}

R/10_plot_ref.R

@@ -23,10 +23,17 @@ plot_ref <- function(df, title_text, join_col, pt_size, use_raster) {
   }
   p + scale_color_identity() +
     geom_text_repel(data = centroids, aes(label = .data[[join_col]]),
-                    size = 3.5, fontface = "bold", bg.color = "white",
+                    family = "Helvetica", fontface = "plain",
+                    size = 6, bg.color = "white",
                     bg.r = 0.1, min.segment.length = 0) +
+    # UMAP dimensions carry no numeric meaning -- remove breaks at the scale
+    # level so the global theme cascade can't reintroduce tick labels.
+    scale_x_continuous(breaks = NULL) +
+    scale_y_continuous(breaks = NULL) +
     coord_equal() + labs(title = title_text, x = NULL, y = NULL) +
     theme_minimal() +
-    theme(panel.grid = element_blank(), axis.text = element_blank(),
+    theme(panel.grid = element_blank(),
+          axis.text  = element_blank(),
+          axis.ticks = element_blank(),
           plot.title = element_text(face = "bold"))
 }

R/11_plot_beta.R

@@ -35,11 +35,22 @@ plot_beta <- function(df, title, pt_size, join_col, show_legend = TRUE,
   }
 
   p <- p + scale_color_gradientn(colors = colors_beta,
-                                 limits = c(-b_max, b_max), na.value = "grey50",
+                                 limits = c(-b_max, b_max), na.value = "#dadada",
                                  name = "Beta",
                                  values = c(0.0, 0.20, 0.45, 0.5, 0.55, 0.80, 1.0)) +
-    coord_equal() + labs(title = title, x = NULL, y = NULL) + theme_minimal() +
-    theme(panel.grid = element_blank(), axis.text = element_blank(),
+    # UMAP_1 / UMAP_2 axes carry no numeric meaning, so remove their breaks
+    # at the SCALE level. Doing it via theme(axis.text = element_blank())
+    # alone is not enough because the outer `& big_helvetica_theme()`
+    # cascade later overrides axis.text and resurrects the tick labels.
+    scale_x_continuous(breaks = NULL) +
+    scale_y_continuous(breaks = NULL) +
+    # `clip = "off"` lets the ggrepel cell-type centroid labels draw past
+    # the panel edge -- at the bigger Helvetica size they sometimes start
+    # near the panel boundary and get truncated (e.g. "T_CD4_C" instead of
+    # "T_CD4_CM").
+    coord_equal(clip = "off") + labs(title = title, x = NULL, y = NULL) + theme_minimal() +
+    theme(panel.grid = element_blank(),
+          axis.text = element_blank(), axis.ticks = element_blank(),
           plot.title  = element_text(size = 8.5, face = "bold"),
           legend.title = element_text(size = 12, face = "bold"),
           legend.text = element_text(size = 10))
@@ -59,8 +70,9 @@ plot_beta <- function(df, title, pt_size, join_col, show_legend = TRUE,
     }
     p <- p + geom_text_repel(data = centroids,
                              aes(x = UMAP_1, y = UMAP_2, label = label_text),
-                             inherit.aes = FALSE, size = 4.5,
-                             fontface = "bold", bg.color = "white", bg.r = 0.15,
+                             inherit.aes = FALSE, size = 7.5,
+                             family = "Helvetica", fontface = "plain",
+                             bg.color = "white", bg.r = 0.15,
                              color = "black", min.segment.length = 0)
   }
   return(p)

R/12_plot_zscore.R

@@ -69,7 +69,7 @@ plot_zscore_df <- function(df, title = "Coloc Z-Scores", panel_cs_label = NULL)
     geom_abline(slope = 1, intercept = 0, color = "gray80", linetype = "dotted") +
     geom_abline(slope = -1, intercept = 0, color = "gray80", linetype = "dotted") +
     geom_point(fill = "#1E90FF", color = "white", shape = 21,
-               size = 2.5, alpha = 0.8, stroke = 0.3) +
+               size = 3.5, alpha = 0.8, stroke = 0.3) +
     coord_fixed(xlim = c(-limit_val, limit_val), ylim = c(-limit_val, limit_val)) +
     theme_minimal() +
     labs(title = title, x = "QTL Z-Score", y = "Disease Z-Score") +

R/13_plot_zoom.R

@@ -81,7 +81,8 @@ plot_zoom_annotations <- function(anno_win, chr_label, lead_pos, win_half,
   } else {
     p <- p + annotate("text", x = lead_pos, y = (n_tracks + 1) / 2,
                       label = "No annotations in window",
-                      size = 3.2, color = "gray55", fontface = "italic")
+                      family = "Helvetica", fontface = "italic",
+                      size = 5, color = "gray55")
   }
   # Row guides on top of rects so each bar lines up with its y-axis label.
   p <- p + geom_hline(yintercept = seq_len(n_tracks), colour = "gray58",
@@ -208,7 +209,8 @@ build_merged_zoom_box <- function(chr_label, lead_positions,
     p <- p + annotate("text",
                       x = mean(lead_positions), y = (n_tracks + 1) / 2,
                       label = "No annotations in merged window",
-                      size = 3.2, color = "gray55", fontface = "italic")
+                      family = "Helvetica", fontface = "italic",
+                      size = 5, color = "gray55")
   }
   p <- p + geom_hline(yintercept = seq_len(n_tracks), colour = "gray58",
                       linewidth = 0.2, alpha = 0.88)
@@ -236,7 +238,9 @@ build_merged_zoom_box <- function(chr_label, lead_positions,
                         alpha = 0.95, linewidth = 0.7)
     p <- p + geom_text_repel(data = extra_df,
                              aes(x = lead, y = n_tracks + 1.3, label = label),
-                             color = "#BF4F00", size = 2.7, fontface = "bold",
+                             color = "#BF4F00",
+                             family = "Helvetica", fontface = "plain",
+                             size = 5,
                              direction = "y", nudge_y = 0.2,
                              segment.size = 0.3, segment.alpha = 0.6,
                              box.padding = 0.25, point.padding = 0.1,