From b6e736c6f639d23ec230db4d7aa2612f706a6470 Mon Sep 17 00:00:00 2001
From: Ivo Kwee <ivo.kwee@gmail.com>
Date: Fri, 16 Jan 2026 11:52:50 +0100
Subject: [PATCH] feat: enhance volcano plot and multipartite graph plotting
 functions
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ggVolcano improvements:
- Add xlim parameter for manual x-axis limit control
- Add ggrepel.padding parameter (default: 0.1) for label spacing control
- Change max.overlaps from 20 to Inf to show all labels without limit
- Improve axis scaling for better plot aesthetics:
  - Y-axis: add 5% top padding (0.05 expansion)
  - X-axis: symmetric 7% padding on both sides (0.07, 0.07)
- Auto-calculate xlim from data range if not specified

plotMultiPartiteGraph2 improvements:
- Make edge.sign parameter options explicit: "both", "pos", "neg", "consensus"
- Make edge.type parameter options explicit: "both", "inter", "intra", "both2"
- Improved self-documenting code showing all available options

These changes improve:
- Label visibility and customization in volcano plots
- Plot margin handling and aesthetics
- Code documentation and usability

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
---
 R/pgx-plotting.R | 19 ++++++++++++++-----
 1 file changed, 14 insertions(+), 5 deletions(-)

diff --git a/R/pgx-plotting.R b/R/pgx-plotting.R
index 76cf0456..50152381 100644
--- a/R/pgx-plotting.R
+++ b/R/pgx-plotting.R
@@ -1305,7 +1305,8 @@ ggVolcano <- function(x,
                       ylab = "significance (-log10q)",
                       lfc = 1,
                       psig = 0.05,
-                      ylim = NULL,
+                      xlim = NULL,
+                      ylim = NULL,                      
                       showlegend = TRUE,
                       marker.size = 2.5,
                       marker.alpha = 0.7,
@@ -1319,6 +1320,7 @@ ggVolcano <- function(x,
                         notsel = "#cccccc88",
                         down = "#3181de"
                       ),
+                      ggrepel.padding = 0.1,
                       girafe = FALSE) {
   if (is.null(highlight)) highlight <- names
   if (showlegend) {
@@ -1346,6 +1348,7 @@ ggVolcano <- function(x,
   df$name <- gsub("[\\'\\`-]", "", df$name)
 
   if (is.null(ylim)) ylim <- max(y, na.rm = TRUE) * 1.1
+  if (is.null(xlim)) xlim <- range(x, na.rm = TRUE)  
 
   plt <- ggplot2::ggplot(df, ggplot2::aes(x = fc, y = y)) +
     ggplot2::geom_point(
@@ -1425,7 +1428,8 @@ ggVolcano <- function(x,
   plt <- plt +
     ggrepel::geom_label_repel(
       ggplot2::aes(label = label, color = category),
-      size = label.cex, family = "lato", box.padding = 0.1, max.overlaps = 20, show.legend = FALSE
+      size = label.cex, family = "lato", box.padding = ggrepel.padding,
+      max.overlaps = Inf, show.legend = FALSE
     )
 
   plt <- plt +
@@ -1434,9 +1438,12 @@ ggVolcano <- function(x,
     ggplot2::geom_vline(xintercept = 0, linetype = "solid", color = "darkgrey") +
     ggplot2::scale_y_continuous(
       limits = c(0, ylim),
-      expand = ggplot2::expansion(mult = c(0, 0))
+      expand = ggplot2::expansion(mult = c(0, 0.05))
+    ) +
+    ggplot2::scale_x_continuous(
+      limits = xlim,
+      expand = ggplot2::expansion(mult = c(0.07, 0.07))
     ) +
-    ggplot2::scale_x_continuous(expand = ggplot2::expansion(mult = c(0.1, 0))) +
     ggplot2::labs(x = xlab, y = ylab) +
     guides(colour = guide_legend(reverse = T)) +
     ggplot2::theme_minimal(base_size = 15) +
@@ -7120,7 +7127,8 @@ plotMultiPartiteGraph2 <- function(graph, layers = NULL,
                                    xpos = NULL, xlim = NULL, justgraph = FALSE,
                                    edge.cex = 1, edge.alpha = 0.33, xdist = 1,
                                    normalize.edges = FALSE, yheight = 2,
-                                   edge.sign = "both", edge.type = "both",
+                                   edge.sign = c("both","pos","neg","consensus")[1],
+                                   edge.type = c("both","inter","intra","both2")[1],
                                    labpos = NULL, value.name = NULL,
                                    strip.prefix = FALSE, strip.prefix2 = FALSE,
                                    prune = FALSE,
@@ -7511,3 +7519,4 @@ plotAdjacencyMatrixFromGraph <- function(graph, nmax = 40, binary = FALSE,
     sym = TRUE, ...
   )
 }
+