From e171f8178b31bae1f55e9b7f8643d6f2e1ac619a Mon Sep 17 00:00:00 2001
From: Ashton Trey Belew <abelew@gmail.com>
Date: Wed, 13 Aug 2025 16:02:09 -0400
Subject: [PATCH] Added a small function 'GetGeneGroupPadded' to avoid
 overlapping gene labels.

---
 R/geom_gene.R |  5 +++--
 R/utils.R     | 26 ++++++++++++++++++++++++++
 2 files changed, 29 insertions(+), 2 deletions(-)

diff --git a/R/geom_gene.R b/R/geom_gene.R
index e707819..4e70394 100644
--- a/R/geom_gene.R
+++ b/R/geom_gene.R
@@ -223,6 +223,8 @@ ggplot_add.gene <- function(object, plot, object_name) {
     gene.group.idx <- GetGeneGroup(used.gene.gr, overlap.gene.gap = overlap.gene.gap)
   } else if (overlap.style == "tight") {
     gene.group.idx <- GetGeneGroupTight(used.gene.gr, overlap.gene.gap = overlap.gene.gap)
+  } else if (overlap.style == "padded") {
+    gene.group.idx <- GetGeneGroupPadded(used.gene.gr, overlap.gene.gap = overlap.gene.gap)
   }
   group.num <- length(unique(gene.group.idx))
   gene.info.used.gene$group <- gene.group.idx
@@ -326,8 +328,7 @@ ggplot_add.gene <- function(object, plot, object_name) {
     geom_text(
       data = label.df,
       mapping = aes_string(x = "pos", y = "group", label = "gene"),
-      vjust = label.vjust, size = label.size
-    ) +
+      vjust = label.vjust, size = label.size) +
     labs(y = "Gene") +
     theme_gene(
       overlap.gene.gap = overlap.gene.gap, group.num = group.num,
diff --git a/R/utils.R b/R/utils.R
index 64e4d5a..79c9307 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -106,6 +106,32 @@ GetGeneGroup <- function(gene.gr, fc = "queryHits", sc = "subjectHits", overlap.
   return(group.idx)
 }
 
+GetGeneGroupPadded <- function(gene.gr, fc = "queryHits", sc = "subjectHits", overlap.gene.gap = 1,
+                               padding = 100) {
+  overlap.gr <- gene.gr
+  end(overlap.gr) <- end(overlap.gr) + padding
+  overlap.df <- IRanges::findOverlaps(overlap.gr, overlap.gr, ignore.strand = TRUE) %>%
+    as.data.frame() %>%
+    dplyr::arrange(.data[[fc]], .data[[sc]])
+  overlap.list <- lapply(split(overlap.df, overlap.df[, fc]), function(x) {
+    x[, sc]
+  })
+  overlap.list <- overlap.list[order(sapply(overlap.list, length), decreasing = TRUE)]
+  group.idx <- rep(1, length(unique(overlap.df[, fc])))
+  for (i in names(overlap.list)) {
+    overlap.vec <- overlap.list[[i]]
+    i <- as.numeric(i)
+    curr.group <- group.idx[i]
+    remain.vec <- setdiff(overlap.vec, i)
+    for (j in remain.vec) {
+      if (group.idx[j] == curr.group) {
+        group.idx[j] <- curr.group + overlap.gene.gap
+      }
+    }
+  }
+  return(group.idx)
+}
+
 # place non-overlapping transcripts together
 GetGeneGroupTight <- function(gene.gr, overlap.gene.gap = 1) {
   # convert to dataframe