From 86583997c92baaa2b7dc31df2972412d244e9f14 Mon Sep 17 00:00:00 2001
From: jahn <jahn@mpusp.mpg.de>
Date: Thu, 4 Jul 2024 14:33:25 +0200
Subject: [PATCH 1/6] fix: typos in color scale

---
 R/geom_coverage.R | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/R/geom_coverage.R b/R/geom_coverage.R
index 6bc5d96..af33518 100644
--- a/R/geom_coverage.R
+++ b/R/geom_coverage.R
@@ -126,9 +126,9 @@ geom_coverage <- function(data, mapping = NULL, color = NULL, rect.color = NA,
         if (is.null(names(fill.color))) {
           names(fill.color) <- unique(data[, group.key])
         }
-        sacle_fill_cols <- scale_fill_manual(values = fill.color)
+        scale_fill_cols <- scale_fill_manual(values = fill.color)
       } else {
-        sacle_fill_cols <- NULL
+        scale_fill_cols <- NULL
       }
       if (!single.nuc) {
         mapping <- aes_string(xmin = "start", xmax = "end", ymin = "0", ymax = "score", fill = group.key)
@@ -180,9 +180,9 @@ geom_coverage <- function(data, mapping = NULL, color = NULL, rect.color = NA,
             names(fill.color) <- unique(data[, fill.str])
           }
         }
-        sacle_fill_cols <- scale_fill_manual(values = fill.color)
+        scale_fill_cols <- scale_fill_manual(values = fill.color)
       } else {
-        sacle_fill_cols <- NULL
+        scale_fill_cols <- NULL
       }
     } else if (plot.type == "joint") {
       message("For joint visualization, the mapping should contains start, score, color.")
@@ -255,8 +255,8 @@ geom_coverage <- function(data, mapping = NULL, color = NULL, rect.color = NA,
     plot.ele <- list(region.rect, region.facet)
 
     # color the track
-    if (!is.null(sacle_fill_cols)) {
-      plot.ele <- append(plot.ele, sacle_fill_cols)
+    if (!is.null(scale_fill_cols)) {
+      plot.ele <- append(plot.ele, scale_fill_cols)
     }
 
     if (range.position == "in") {

From e1857766600847fa4673fcf6d18a39a6a5a0e79d Mon Sep 17 00:00:00 2001
From: jahn <jahn@mpusp.mpg.de>
Date: Thu, 4 Jul 2024 14:34:03 +0200
Subject: [PATCH 2/6] feat: added functions to customize colors in geom_peak

---
 DESCRIPTION       |   2 +-
 NAMESPACE         |   1 +
 R/geom_coverage.R |  10 ++--
 R/geom_feature.R  |   2 +-
 R/geom_peak.R     | 133 +++++++++++++++++++++++++++++-----------------
 R/utils.R         |  12 ++---
 man/geom_peak.Rd  |  75 ++++++++++++++++----------
 7 files changed, 145 insertions(+), 90 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 70a3a6a..9f30a29 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -57,4 +57,4 @@ VignetteBuilder:
     knitr
 biocViews:
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
diff --git a/NAMESPACE b/NAMESPACE
index a59ad92..9c56902 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -114,6 +114,7 @@ importFrom(ggplot2,ggplot_add)
 importFrom(ggplot2,labs)
 importFrom(ggplot2,margin)
 importFrom(ggplot2,rel)
+importFrom(ggplot2,scale_color_continuous)
 importFrom(ggplot2,scale_color_gradientn)
 importFrom(ggplot2,scale_color_manual)
 importFrom(ggplot2,scale_fill_manual)
diff --git a/R/geom_coverage.R b/R/geom_coverage.R
index af33518..2556a43 100644
--- a/R/geom_coverage.R
+++ b/R/geom_coverage.R
@@ -119,7 +119,7 @@ geom_coverage <- function(data, mapping = NULL, color = NULL, rect.color = NA,
         if (length(color) < length(unique(data[, group.key]))) {
           warning("Fewer colors provided than there are groups in ", group.key, " variable, falling back to default colors")
           # sample group with same color
-          fill.color <- AutoColor(data = data, n = 9, name = "Set1", key = group.key)
+          fill.color <- AutoColor(data = data[[group.key]], pal = "Set1")
         } else {
           fill.color <- color
         }
@@ -140,7 +140,7 @@ geom_coverage <- function(data, mapping = NULL, color = NULL, rect.color = NA,
         if (length(color) != length(unique(data[, group.key]))) {
           warning("The color you provided is not as long as ", group.key, " column in data, select automatically!")
           # sample group with same color
-          tmp.color <- AutoColor(data = data, n = 9, name = "Set1", key = group.key)
+          tmp.color <- AutoColor(data = data[[group.key]], pal = "Set1")
           # change group key color
           color.color.df <- merge(unique(data[c(group.key)]), data.frame(color = tmp.color), by.x = group.key, by.y = 0)
           color.color <- color.color.df$color
@@ -169,7 +169,7 @@ geom_coverage <- function(data, mapping = NULL, color = NULL, rect.color = NA,
         fill.str.len <- length(unique(data[, fill.str]))
         if (is.null(color) | length(color) != fill.str.len) {
           # sample group with same color
-          tmp.color <- AutoColor(data = data, n = 9, name = "Set1", key = group.key)
+          tmp.color <- AutoColor(data = data[[group.key]], pal = "Set1")
           # change color
           fill.color.df <- merge(unique(data[c(fill.str, group.key)]), data.frame(color = tmp.color), by.x = group.key, by.y = 0)
           fill.color <- fill.color.df$color
@@ -191,7 +191,7 @@ geom_coverage <- function(data, mapping = NULL, color = NULL, rect.color = NA,
         color.str.len <- length(unique(data[, color.str]))
         if (is.null(color) | length(color) != color.str.len) {
           # sample group with same color
-          tmp.color <- AutoColor(data = data, n = 9, name = "Set1", key = group.key)
+          tmp.color <- AutoColor(data = data[[group.key]], pal = "Set1")
           # change color
           if (color.str == group.key) {
             color.color.df <- merge(unique(data[c(color.str)]), data.frame(color = tmp.color), by.x = group.key, by.y = 0)
@@ -223,7 +223,7 @@ geom_coverage <- function(data, mapping = NULL, color = NULL, rect.color = NA,
 
     # facet color
     if (is.null(facet.color)) {
-      facet.color <- AutoColor(data = data, n = 12, name = "Set3", key = facet.key)
+      facet.color <- AutoColor(data = data[[facet.key]], pal = "Set3")
     }
 
     # facet formula
diff --git a/R/geom_feature.R b/R/geom_feature.R
index 7565fbe..0ee0196 100644
--- a/R/geom_feature.R
+++ b/R/geom_feature.R
@@ -99,7 +99,7 @@ ggplot_add.feature <- function(object, plot, object_name) {
     }
   } else {
     warning("The color you provided is smaller than Type column in data, select automatically!")
-    used.feature.color <- AutoColor(data = valid.feature, n = 9, name = "Set1", key = "Type")
+    used.feature.color <- AutoColor(data = valid.feature$Type, pal = "Set1")
   }
 
   # create plot
diff --git a/R/geom_peak.R b/R/geom_peak.R
index 2a33ca5..b5e40e8 100644
--- a/R/geom_peak.R
+++ b/R/geom_peak.R
@@ -2,51 +2,69 @@
 #'
 #' @param bed.file The path to consensus peaks file. Default: NULL.
 #' @param peak.df The dataframe contains consensus peaks. Default: NULL.
-#' @param peak.color Peak color. Default: black.
+#' @param peak.color Peak colors. Default: NULL.
 #' @param peak.size The line size of peak. Default: 5.
+#' @param color.by Name of optional column in bed file/data frame which is used for coloring. Default: NULL.
 #' @param plot.space Top and bottom margin. Default: 0.1.
-#' @param plot.height The relative height of peak annotation to coverage plot. Default: 0.2.
+#' @param plot.height The relative height of peak annotation to coverage plot. Default: 0.1.
 #'
 #' @return Plot.
 #' @importFrom utils read.table
 #' @importFrom dplyr arrange
 #' @importFrom dplyr %>%
-#' @importFrom ggplot2 ggplot_add ggplot geom_segment aes_string theme_classic theme element_blank element_text
-#' element_rect margin scale_x_continuous scale_y_continuous coord_cartesian
+#' @importFrom ggplot2 ggplot_add ggplot geom_segment aes_string theme_classic
+#'   theme element_blank element_text element_rect margin scale_x_continuous
+#'   scale_y_continuous scale_color_continuous coord_cartesian
 #' @export
 #'
 #' @examples
-#' # library(ggcoverage)
-#' # library(rtracklayer)
-#' # sample.meta <- data.frame(
-#' #   SampleName = c("Chr18_MCF7_ER_1", "Chr18_MCF7_ER_2", "Chr18_MCF7_ER_3", "Chr18_MCF7_input"),
-#' #   Type = c("MCF7_ER_1", "MCF7_ER_2", "MCF7_ER_3", "MCF7_input"),
-#' #   Group = c("IP", "IP", "IP", "Input")
-#' # )
-#' # track folder
-#' # track.folder <- system.file("extdata", "ChIP-seq", package = "ggcoverage")
-#' # load bigwig file
-#' # track.df <- LoadTrackFile(
-#' #   track.folder = track.folder, format = "bw",
-#' #   meta.info = sample.meta
-#' # )
-#' # gtf.file <- system.file("extdata", "used_hg19.gtf", package = "ggcoverage")
-#' # gtf.gr <- rtracklayer::import.gff(con = gtf.file, format = "gtf")
-#' # create mark region
-#' # mark.region <- data.frame(start = c(76822533), end = c(76823743), label = c("Promoter"))
-#' # basic.coverage <- ggcoverage(
-#' #   data = track.df, color = "auto", region = "chr18:76822285-76900000",
-#' #   mark.region = mark.region, show.mark.label = FALSE
-#' # )
-#' # get consensus peak file
-#' # peak.file <- system.file("extdata", "ChIP-seq", "consensus.peak", package = "ggcoverage")
-#' # basic.coverage + geom_gene(gtf.gr = gtf.gr) + geom_peak(bed.file = peak.file)
-geom_peak <- function(bed.file = NULL, peak.df = NULL, peak.color = "black", peak.size = 5,
-                      plot.space = 0.1, plot.height = 0.1) {
+#' # load metadata
+#' sample_meta <- data.frame(
+#'   SampleName = c(
+#'     "Chr18_MCF7_ER_1",
+#'     "Chr18_MCF7_ER_2",
+#'     "Chr18_MCF7_ER_3",
+#'     "Chr18_MCF7_input"
+#'   ),
+#'   Type = c("MCF7_ER_1", "MCF7_ER_2", "MCF7_ER_3", "MCF7_input"),
+#'   Group = c("IP", "IP", "IP", "Input")
+#' )
+#'
+#' # import coverage track
+#' track_folder <- system.file("extdata", "ChIP-seq", package = "ggcoverage")
+#' track_df <- LoadTrackFile(
+#'   track.folder = track_folder,
+#'   format = "bw",
+#'   region = "chr18:76822285-76900000",
+#'   meta.info = sample_meta
+#' )
+#'
+#' # create mock peak file
+#' df_peaks <- data.frame(
+#'   seqnames = c("chr18", "chr18", "chr18"),
+#'   start = c(76822533, 76846900, 76880000),
+#'   end = c(76836900, 76860000, 76887000),
+#'   score = c(4, 6, 13)
+#' )
+#'
+#' # plot with default color
+#' ggcoverage(data = track_df) +
+#'   geom_peak(peak.df = df_peaks, peak.size = 3)
+#'
+#' # plot with color by 'score' variable
+#' ggcoverage(data = track_df) +
+#'   geom_peak(peak.df = df_peaks, peak.size = 3, color.by = "score")
+#'
+#' # plot with color by 'score' variable and custom color scale
+#' ggcoverage(data = track_df) +
+#'   geom_peak(peak.df = df_peaks, peak.size = 3, color.by = "score", peak.color = rainbow(5))
+#'
+geom_peak <- function(bed.file = NULL, peak.df = NULL, peak.color = NULL, peak.size = 5,
+                      color.by = NULL, plot.space = 0.1, plot.height = 0.1) {
   structure(
     list(
       bed.file = bed.file, peak.df = peak.df, peak.color = peak.color, peak.size = peak.size,
-      plot.space = plot.space, plot.height = plot.height
+      color.by = color.by, plot.space = plot.space, plot.height = plot.height
     ),
     class = "peak"
   )
@@ -54,22 +72,13 @@ geom_peak <- function(bed.file = NULL, peak.df = NULL, peak.color = "black", pea
 
 #' @export
 ggplot_add.peak <- function(object, plot, object_name) {
-  # get plot data
-  # plot.data <- plot$layers[[1]]$data
-  # get plot data, plot data should contain bins
   if ("patchwork" %in% class(plot)) {
     plot.data <- plot[[1]]$layers[[1]]$data
   } else {
     plot.data <- plot$layers[[1]]$data
   }
-  # prepare plot range
-  # the plot region are not normal, so start is minimum value
   plot.chr <- as.character(plot.data[1, "seqnames"])
-  # plot.region.start <- plot$coordinates$limits$x[1]
-  # plot.region.end <- plot$coordinates$limits$x[2]
-  # plot.region.start <- plot.data[1, "start"]
   plot.region.start <- min(plot.data[, "start"])
-  # plot.region.end <- plot.data[nrow(plot.data), "end"]
   plot.region.end <- max(plot.data[, "end"])
 
   # get parameters
@@ -77,6 +86,7 @@ ggplot_add.peak <- function(object, plot, object_name) {
   peak.df <- object$peak.df
   peak.color <- object$peak.color
   peak.size <- object$peak.size
+  color.by <- object$color.by
   plot.space <- object$plot.space
   plot.height <- object$plot.height
 
@@ -86,14 +96,36 @@ ggplot_add.peak <- function(object, plot, object_name) {
   } else if (!is.null(peak.df)) {
     bed.info <- peak.df
   }
-  bed.info <- bed.info[c(1, 2, 3)]
-  colnames(bed.info) <- c("seqnames", "start", "end")
-  # convert to 1-based
+  colnames(bed.info)[c(1, 2, 3)] <- c("seqnames", "start", "end")
   bed.info$start <- as.numeric(bed.info$start) + 1
-
-  # get valid bed
   valid.bed <- GetRegion(chr = plot.chr, df = bed.info, start = plot.region.start, end = plot.region.end)
 
+  # color management
+  if (!is.null(color.by)) {
+    if (is.numeric(valid.bed[[color.by]])) {
+      if (!is.null(peak.color)) {
+        scale_colors <- scale_color_gradientn(colours = peak.color)
+      } else {
+        scale_colors <- scale_color_continuous()
+      }
+    } else {
+      if (length(peak.color) < length(unique(valid.bed[[color.by]]))) {
+        warning("Fewer colors provided than there are groups in ", color.by, " variable, falling back to default colors")
+        auto_colors <- AutoColor(data = valid.bed[[color.by]], pal = "Set3")
+        scale_colors <- scale_color_manual(values = auto_colors)
+      } else {
+        scale_colors <- scale_color_manual(values = peak.color)
+      }
+    }
+  } else {
+    color.by <- "color"
+    if (is.null(peak.color)) {
+      peak.color <- "black"
+    }
+    valid.bed$color <- peak.color[1]
+    scale_colors <- scale_color_manual(values = peak.color)
+  }
+
   peak.plot <- ggplot() +
     geom_segment(
       data = valid.bed,
@@ -101,15 +133,18 @@ ggplot_add.peak <- function(object, plot, object_name) {
         x = "start",
         y = "1",
         xend = "end",
-        yend = "1"
+        yend = "1",
+        color = color.by
       ),
       size = peak.size,
-      color = peak.color
     ) +
+    scale_colors +
     labs(y = "Peak")
 
   # add theme
-  peak.plot <- peak.plot + theme_peak(margin.len = plot.space, x.range = c(plot.region.start, plot.region.end))
+  peak.plot <- peak.plot +
+    theme_peak(margin.len = plot.space, x.range = c(plot.region.start, plot.region.end)) +
+    theme(legend.position = "none")
   # assemble plot
   patchwork::wrap_plots(plot + theme(plot.margin = margin(t = plot.space, b = plot.space)),
     peak.plot,
diff --git a/R/utils.R b/R/utils.R
index c4d187c..ae39d01 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -55,18 +55,18 @@ PrepareRegion <- function(region = NULL,
 }
 
 # select color automatically
-AutoColor <- function(data, n, name, key) {
+AutoColor <- function(data, pal) {
   palettes <- list(
     Set1 = c("#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#FFFF33", "#A65628", "#F781BF", "#999999"),
     Set2 = c("#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3"),
     Set3 = c("#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", "#D9D9D9")
   )
-  getPalette <- grDevices::colorRampPalette(palettes[[name]])
+  get_palette <- grDevices::colorRampPalette(palettes[[pal]])
   # sample group with same color
-  group.info <- unique(data[, key])
-  fill.color <- getPalette(length(group.info))
-  names(fill.color) <- group.info
-  return(fill.color)
+  data_levels <- unique(data)
+  cols <- get_palette(length(data_levels))
+  names(cols) <- data_levels
+  return(cols)
 }
 
 # create aa plot dataframe with padding offset
diff --git a/man/geom_peak.Rd b/man/geom_peak.Rd
index 02c87f4..19f8f1c 100644
--- a/man/geom_peak.Rd
+++ b/man/geom_peak.Rd
@@ -7,8 +7,9 @@
 geom_peak(
   bed.file = NULL,
   peak.df = NULL,
-  peak.color = "black",
+  peak.color = NULL,
   peak.size = 5,
+  color.by = NULL,
   plot.space = 0.1,
   plot.height = 0.1
 )
@@ -18,13 +19,15 @@ geom_peak(
 
 \item{peak.df}{The dataframe contains consensus peaks. Default: NULL.}
 
-\item{peak.color}{Peak color. Default: black.}
+\item{peak.color}{Peak colors. Default: NULL.}
 
 \item{peak.size}{The line size of peak. Default: 5.}
 
+\item{color.by}{Name of optional column in bed file/data frame which is used for coloring. Default: NULL.}
+
 \item{plot.space}{Top and bottom margin. Default: 0.1.}
 
-\item{plot.height}{The relative height of peak annotation to coverage plot. Default: 0.2.}
+\item{plot.height}{The relative height of peak annotation to coverage plot. Default: 0.1.}
 }
 \value{
 Plot.
@@ -33,29 +36,45 @@ Plot.
 Add Peak Annotation to Coverage Plot.
 }
 \examples{
-# library(ggcoverage)
-# library(rtracklayer)
-# sample.meta <- data.frame(
-#   SampleName = c("Chr18_MCF7_ER_1", "Chr18_MCF7_ER_2", "Chr18_MCF7_ER_3", "Chr18_MCF7_input"),
-#   Type = c("MCF7_ER_1", "MCF7_ER_2", "MCF7_ER_3", "MCF7_input"),
-#   Group = c("IP", "IP", "IP", "Input")
-# )
-# track folder
-# track.folder <- system.file("extdata", "ChIP-seq", package = "ggcoverage")
-# load bigwig file
-# track.df <- LoadTrackFile(
-#   track.folder = track.folder, format = "bw",
-#   meta.info = sample.meta
-# )
-# gtf.file <- system.file("extdata", "used_hg19.gtf", package = "ggcoverage")
-# gtf.gr <- rtracklayer::import.gff(con = gtf.file, format = "gtf")
-# create mark region
-# mark.region <- data.frame(start = c(76822533), end = c(76823743), label = c("Promoter"))
-# basic.coverage <- ggcoverage(
-#   data = track.df, color = "auto", region = "chr18:76822285-76900000",
-#   mark.region = mark.region, show.mark.label = FALSE
-# )
-# get consensus peak file
-# peak.file <- system.file("extdata", "ChIP-seq", "consensus.peak", package = "ggcoverage")
-# basic.coverage + geom_gene(gtf.gr = gtf.gr) + geom_peak(bed.file = peak.file)
+# load metadata
+sample_meta <- data.frame(
+  SampleName = c(
+    "Chr18_MCF7_ER_1",
+    "Chr18_MCF7_ER_2",
+    "Chr18_MCF7_ER_3",
+    "Chr18_MCF7_input"
+  ),
+  Type = c("MCF7_ER_1", "MCF7_ER_2", "MCF7_ER_3", "MCF7_input"),
+  Group = c("IP", "IP", "IP", "Input")
+)
+
+# import coverage track
+track_folder <- system.file("extdata", "ChIP-seq", package = "ggcoverage")
+track_df <- LoadTrackFile(
+  track.folder = track_folder,
+  format = "bw",
+  region = "chr18:76822285-76900000",
+  meta.info = sample_meta
+)
+
+# create mock peak file
+df_peaks <- data.frame(
+  seqnames = c("chr18", "chr18", "chr18"),
+  start = c(76822533, 76846900, 76880000),
+  end = c(76836900, 76860000, 76887000),
+  score = c(4, 6, 13)
+)
+
+# plot with default color
+ggcoverage(data = track_df) +
+  geom_peak(peak.df = df_peaks, peak.size = 3)
+
+# plot with color by 'score' variable
+ggcoverage(data = track_df) +
+  geom_peak(peak.df = df_peaks, peak.size = 3, color.by = "score")
+
+# plot with color by 'score' variable and custom color scale
+ggcoverage(data = track_df) +
+  geom_peak(peak.df = df_peaks, peak.size = 3, color.by = "score", peak.color = rainbow(5))
+
 }

From 859139c5dd4fca880f7171abd1cfc94810d30bc6 Mon Sep 17 00:00:00 2001
From: jahn <jahn@mpusp.mpg.de>
Date: Wed, 9 Oct 2024 22:04:38 +0200
Subject: [PATCH 3/6] feat: initial draft for styling gene arrows; closes #38

---
 R/geom_gene.R | 94 ++++++++++++++++++++++++++++++++++++---------------
 R/utils.R     | 73 ++++++++++++++-------------------------
 2 files changed, 91 insertions(+), 76 deletions(-)

diff --git a/R/geom_gene.R b/R/geom_gene.R
index 8424399..5747662 100644
--- a/R/geom_gene.R
+++ b/R/geom_gene.R
@@ -4,10 +4,14 @@
 #' @param overlap.gene.gap The gap between gene groups. Default: 0.1.
 #' @param overlap.style The style of gene groups, choose from loose (each gene occupies single line)
 #' and tight (place non-overlap genes in one line). Default: loose.
-#' @param gene.size The line size of gene. Default: 1.
-#' @param utr.size The line size of UTR. Default: 2.
-#' @param exon.size The line size of exon. Default: 3.
-#' @param arrow.size The line size of arrow. Default: 1.5.
+#' @param gene.size The line width of genes. Default: 1.
+#' @param utr.size The line width of UTRs. Default: 2.
+#' @param exon.size The line width of exons. Default: 3.
+#' @param arrow.angle Angle of the arrow head. Default 35°
+#' @param arrow.length Length of arrows. Default: 1.5
+#' @param arrow.type Whether to draw "closed" or "open" (default) arrow heads
+
+#' @param
 #' @param arrow.gap The gap distance between intermittent arrows. Default: NULL.
 #'   Set arrow.num and arrow.gap to NULL to suppress intermittent arrows.
 #' @param arrow.num Total number of intermittent arrows over whole region. Default: 50.
@@ -21,6 +25,13 @@
 #' @param plot.space Top and bottom margin. Default: 0.1.
 #' @param plot.height The relative height of gene annotation to coverage plot. Default: 0.2.
 #'
+
+arrow.gap = NULL,
+arrow.num = 50,
+arrow.size.im = 0.5,
+arrow.length.im = 1.5,
+arrow.type.im = "closed",
+color.by.im = NULL,
 #' @return Plot.
 #' @importFrom dplyr %>%
 #' @importFrom rlang .data
@@ -61,16 +72,37 @@
 #' basic.coverage <- ggcoverage(data = track_df, range.position = "out")
 #' basic.coverage +
 #'   geom_gene(gtf.gr = gtf_gr)
+#'
+#'# plot with custom style
+#' basic_coverage +
+#'   geom_gene(
+#'     gtf.gr = gtf_gr,
+#'     exon.size = 2.0,
+#'     arrow.size.im = 1.0,
+#'     arrow.length.im = 5,
+#'     arrow.type.im = "open",
+#'     color.by.im = "strand",
+#'     fill.color = c(
+#'       "-" = "darkblue",
+#'       "+" = "darkgreen"
+#'     )
+#'   )
 geom_gene <- function(gtf.gr,
                       overlap.gene.gap = 0.1,
                       overlap.style = "loose",
                       gene.size = 1,
                       utr.size = 2,
                       exon.size = 3,
-                      arrow.size = 1.5,
+                      arrow.angle = 35,
+                      arrow.length = 1.5,
+                      arrow.type = "open",
+                      color.by = "strand",
                       arrow.gap = NULL,
                       arrow.num = 50,
-                      color.by = "strand",
+                      arrow.size.im = 0.5,
+                      arrow.length.im = 1.5,
+                      arrow.type.im = "closed",
+                      color.by.im = NULL,
                       fill.color = c(
                         "-" = "cornflowerblue",
                         "+" = "darkolivegreen3"
@@ -88,10 +120,16 @@ geom_gene <- function(gtf.gr,
       gene.size = gene.size,
       utr.size = utr.size,
       exon.size = exon.size,
-      arrow.size = arrow.size,
+      arrow.angle = arrow.angle,
+      arrow.length = arrow.length,
+      arrow.type = arrow.type,
+      color.by = color.by,
       arrow.gap = arrow.gap,
       arrow.num = arrow.num,
-      color.by = color.by,
+      arrow.size.im = arrow.size.im,
+      arrow.length.im = arrow.length.im,
+      arrow.type.im = arrow.type.im,
+      color.by.im = color.by.im,
       fill.color = fill.color,
       show.utr = show.utr,
       label.size = label.size,
@@ -121,22 +159,9 @@ ggplot_add.gene <- function(object, plot, object_name) {
     ranges = IRanges::IRanges(plot.range.start, plot.range.end)
   )
   # get parameters
-  gtf.gr <- object$gtf.gr
-  overlap.gene.gap <- object$overlap.gene.gap
-  overlap.style <- object$overlap.style
-  gene.size <- object$gene.size
-  utr.size <- object$utr.size
-  exon.size <- object$exon.size
-  arrow.size <- object$arrow.size
-  color.by <- object$color.by
-  fill.color <- object$fill.color
-  show.utr <- object$show.utr
-  arrow.gap <- object$arrow.gap
-  arrow.num <- object$arrow.num
-  label.size <- object$label.size
-  label.vjust <- object$label.vjust
-  plot.space <- object$plot.space
-  plot.height <- object$plot.height
+  for (ob in names(object)) {
+    assign(x = ob, value = object[[ob]])
+  }
 
   # get gene in region
   gtf.df.used <- IRanges::subsetByOverlaps(x = gtf.gr, ranges = plot.range.gr) %>% as.data.frame()
@@ -203,11 +228,11 @@ ggplot_add.gene <- function(object, plot, object_name) {
     gene.info.used.utr <- gene.exon.utr$utr
   }
   gene.plot <- ggplot() +
-    geom_arrows(gene.info.used.gene, color.by, gene.size, arrow.size) +
-    geom_arrows(gene.info.used.exon, color.by, exon.size, arrow.size)
+    geom_arrows(gene.info.used.gene, color.by, gene.size, arrow.length, arrow.angle, arrow.type) +
+    geom_arrows(gene.info.used.exon, color.by, exon.size, arrow.length, arrow.angle, arrow.type)
   if (show.utr) {
     gene.plot <- gene.plot +
-      geom_arrows(gene.info.used.utr, color.by, utr.size, arrow.size)
+      geom_arrows(gene.info.used.utr, color.by, utr.size, arrow.length, arrow.angle, arrow.type)
   }
 
   if (!is.null(arrow.gap) || !is.null(arrow.num)) {
@@ -251,8 +276,21 @@ ggplot_add.gene <- function(object, plot, object_name) {
     arrow.df$start <- as.numeric(arrow.df$start)
     arrow.df$end <- as.numeric(arrow.df$end)
     arrow.df$group <- as.numeric(arrow.df$group)
+    if (is.null(color.by.im)) {
+      color.by.im <- color.by
+      arrow.df[[color.by]] <- "im"
+      fill.color["im"] <- grDevices::grey(1, alpha = 0.5)
+    } else if (color.by.im %in% colnames(arrow.df)) {
+      stopifnot(unique(arrow.df[[color.by.im]]) %in% names(fill.color))
+    } else {
+      stop(paste0(
+        "The selected variable '",
+        color.by.im ,
+        "' for 'color.by.im' is not available in the data"
+      ))
+    }
     gene.plot <- gene.plot +
-      geom_arrows(arrow.df, color.by, gene.size / 2, arrow.size, 35, TRUE)
+      geom_arrows(arrow.df, color.by.im, arrow.size.im, arrow.length.im, arrow.angle, arrow.type.im)
   }
 
   label.df <- data.frame(
diff --git a/R/utils.R b/R/utils.R
index ae39d01..9a755cd 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -355,9 +355,8 @@ GetPlotData <- function(plot, layer.num = 1) {
 #' @param color name of the color column in the data frame
 #' @param line_width line_width of the (arrow) segment
 #' @param arrow_size size of the arrow
-#' @param arrow_angle angle of the arrow. Default: 35°
-#' @param intermittent If TRUE, arrows are only drawn intermittently in
-#'   half-transparent white color. Default: FALSE.
+#' @param arrow_angle angle of the arrow in degrees
+#' @param arrow_type type of arrow, either 'open' or 'closed'
 #' @importFrom grDevices grey
 #' @return A geom layer for ggplot2 objects.
 #' @export
@@ -366,54 +365,32 @@ geom_arrows <-
            color,
            line_width,
            arrow_size,
-           arrow_angle = 35,
-           intermittent = FALSE) {
+           arrow_angle,
+           arrow_type) {
     if (nrow(data)) {
       if (!"strand" %in% colnames(data)) {
         data$strand <- "+"
       }
-      if (!intermittent) {
-        geom_segment(
-          data = data,
-          mapping = aes_string(
-            x = "start",
-            y = "group",
-            xend = "end",
-            yend = "group",
-            color = color
-          ),
-          arrow = arrow(
-            ends = ifelse(data$strand == "+", "last", "first"),
-            angle = arrow_angle,
-            length = unit(arrow_size, "points"),
-            type = "open"
-          ),
-          lineend = "butt",
-          linejoin = "mitre",
-          show.legend = FALSE,
-          linewidth = line_width
-        )
-      } else {
-        geom_segment(
-          data = data,
-          mapping = aes_string(
-            x = "start",
-            y = "group",
-            xend = "end",
-            yend = "group"
-          ),
-          arrow = arrow(
-            ends = ifelse(data$strand == "+", "last", "first"),
-            angle = arrow_angle,
-            length = unit(arrow_size, "points"),
-            type = "closed"
-          ),
-          lineend = "butt",
-          linejoin = "mitre",
-          show.legend = FALSE,
-          linewidth = line_width,
-          color = grDevices::grey(1, alpha = 0.5)
-        )
-      }
+      geom_segment(
+        inherit.aes = TRUE,
+        data = data,
+        mapping = aes(
+          x = .data[["start"]],
+          y = .data[["group"]],
+          xend = .data[["end"]],
+          yend = .data[["group"]],
+          color = .data[[color]]
+        ),
+        arrow = arrow(
+          ends = ifelse(data$strand == "+", "last", "first"),
+          angle = arrow_angle,
+          length = unit(arrow_size, "points"),
+          type = arrow_type
+        ),
+        lineend = "butt",
+        linejoin = "mitre",
+        show.legend = FALSE,
+        linewidth = line_width
+      )
     }
   }

From b416a04248cfda227e9f733307f87ef0c7db7b43 Mon Sep 17 00:00:00 2001
From: jahn <jahn@mpusp.mpg.de>
Date: Thu, 10 Oct 2024 11:06:36 +0200
Subject: [PATCH 4/6] feat: further improvements for styling gene arrows #38

---
 R/geom_gene.R          |  77 +++++++++++++--------
 R/geom_transcript.R    | 151 ++++++++++++++++++++++++++++-------------
 R/utils.R              |   1 -
 man/geom_arrows.Rd     |  14 +---
 man/geom_gene.Rd       |  69 +++++++++++++++----
 man/geom_transcript.Rd |  73 +++++++++++++++-----
 6 files changed, 267 insertions(+), 118 deletions(-)

diff --git a/R/geom_gene.R b/R/geom_gene.R
index 5747662..1dfd4ff 100644
--- a/R/geom_gene.R
+++ b/R/geom_gene.R
@@ -1,46 +1,50 @@
 #' Add Gene Annotation to Coverage Plot.
 #'
-#' @param gtf.gr Granges object of GTF, created with \code{\link{import.gff}}. Default: NULL.
+#' @param gtf.gr Granges object of GTF, created with \code{\link{import.gff}}.
+#'   Default: NULL.
 #' @param overlap.gene.gap The gap between gene groups. Default: 0.1.
-#' @param overlap.style The style of gene groups, choose from loose (each gene occupies single line)
-#' and tight (place non-overlap genes in one line). Default: loose.
-#' @param gene.size The line width of genes. Default: 1.
-#' @param utr.size The line width of UTRs. Default: 2.
-#' @param exon.size The line width of exons. Default: 3.
+#' @param overlap.style The style of gene groups, choose from loose (each gene
+#'   occupies single line) and tight (place non-overlap genes in one line).
+#'   Default: loose.
+#' @param gene.size Line width of genes. Default: 1.
+#' @param utr.size Line width of UTRs. Default: 2.
+#' @param exon.size Line width of exons. Default: 3.
 #' @param arrow.angle Angle of the arrow head. Default 35°
 #' @param arrow.length Length of arrows. Default: 1.5
 #' @param arrow.type Whether to draw "closed" or "open" (default) arrow heads
-
-#' @param
+#' @param color.by Color the lines/arrows by variable. Default: "strand".
 #' @param arrow.gap The gap distance between intermittent arrows. Default: NULL.
 #'   Set arrow.num and arrow.gap to NULL to suppress intermittent arrows.
-#' @param arrow.num Total number of intermittent arrows over whole region. Default: 50.
-#'   Set arrow.num and arrow.gap to NULL to suppress intermittent arrows.
-#' @param color.by Color the line by. Default: strand.
+#' @param arrow.num Total number of intermittent arrows over whole region.
+#'   Default: 50. Set arrow.num and arrow.gap to NULL to suppress intermittent
+#'   arrows.
+#' @param arrow.size.im Line width of intermittent arrows. Default: 0.5
+#' @param arrow.length.im Length of intermittent arrows. Default: 1.5
+#' @param arrow.type.im Whether to draw "closed" (default) or "open" heads for
+#'   intermittent arrows
+#' @param color.by.im Color the intermittent arrows by variable. Default: NULL
+#'   (draws semi-transparent, white arrows)
 #' @param fill.color Color used for \code{color.by}.
-#' Default: blue for - (minus strand), green for + (plus strand).
+#'   Default: blue for - (minus strand), green for + (plus strand).
 #' @param show.utr Logical value, whether to show UTR. Default: TRUE.
 #' @param label.size The size of gene label. Default: 3.
 #' @param label.vjust The vjust of gene label. Default: 2.
 #' @param plot.space Top and bottom margin. Default: 0.1.
-#' @param plot.height The relative height of gene annotation to coverage plot. Default: 0.2.
+#' @param plot.height The relative height of gene annotation to coverage plot.
+#'   Default: 0.2.
 #'
-
-arrow.gap = NULL,
-arrow.num = 50,
-arrow.size.im = 0.5,
-arrow.length.im = 1.5,
-arrow.type.im = "closed",
-color.by.im = NULL,
 #' @return Plot.
 #' @importFrom dplyr %>%
 #' @importFrom rlang .data
 #' @importFrom GenomicRanges GRanges makeGRangesFromDataFrame setdiff
 #' @importFrom IRanges IRanges subsetByOverlaps findOverlaps
 #' @importFrom dplyr filter select arrange
-#' @importFrom ggplot2 ggplot_add ggplot geom_segment aes_string arrow unit geom_text labs theme_classic theme element_blank
-#' element_text element_rect margin scale_y_continuous scale_color_manual scale_x_continuous coord_cartesian
+#' @importFrom ggplot2 ggplot_add ggplot geom_segment aes_string arrow unit
+#'   geom_text labs theme_classic theme element_blank element_text element_rect
+#'   margin scale_y_continuous scale_color_manual scale_x_continuous
+#'   coord_cartesian
 #' @importFrom patchwork wrap_plots
+#' @importFrom grDevices grey
 #' @export
 #'
 #' @examples
@@ -69,8 +73,8 @@ color.by.im = NULL,
 #' gtf_gr <- rtracklayer::import.gff(con = gtf_file, format = "gtf")
 #'
 #' # plot coverage and gene annotation
-#' basic.coverage <- ggcoverage(data = track_df, range.position = "out")
-#' basic.coverage +
+#' basic_coverage <- ggcoverage(data = track_df, range.position = "out")
+#' basic_coverage +
 #'   geom_gene(gtf.gr = gtf_gr)
 #'
 #'# plot with custom style
@@ -159,9 +163,28 @@ ggplot_add.gene <- function(object, plot, object_name) {
     ranges = IRanges::IRanges(plot.range.start, plot.range.end)
   )
   # get parameters
-  for (ob in names(object)) {
-    assign(x = ob, value = object[[ob]])
-  }
+  gtf.gr <- object$gtf.gr
+  overlap.gene.gap <- object$overlap.gene.gap
+  overlap.style <- object$overlap.style
+  gene.size <- object$gene.size
+  utr.size <- object$utr.size
+  exon.size <- object$exon.size
+  arrow.angle <- object$arrow.angle
+  arrow.length <- object$arrow.length
+  arrow.type <- object$arrow.type
+  color.by <- object$color.by
+  arrow.gap <- object$arrow.gap
+  arrow.num <- object$arrow.num
+  arrow.size.im <- object$arrow.size.im
+  arrow.length.im <- object$arrow.length.im
+  arrow.type.im <- object$arrow.type.im
+  color.by.im <- object$color.by.im
+  fill.color <- object$fill.color
+  show.utr <- object$show.utr
+  label.size <- object$label.size
+  label.vjust <- object$label.vjust
+  plot.space <- object$plot.space
+  plot.height <- object$plot.height
 
   # get gene in region
   gtf.df.used <- IRanges::subsetByOverlaps(x = gtf.gr, ranges = plot.range.gr) %>% as.data.frame()
diff --git a/R/geom_transcript.R b/R/geom_transcript.R
index ac4a103..d877402 100644
--- a/R/geom_transcript.R
+++ b/R/geom_transcript.R
@@ -1,25 +1,37 @@
 #' Add Transcript Annotation to Coverage Plot.
 #'
-#' @param gtf.gr Granges object of GTF, created with \code{\link{import.gff}}. Default: NULL.
+#' @param gtf.gr Granges object of GTF, created with \code{\link{import.gff}}.
+#'   Default: NULL.
 #' @param gene.name Gene name of all transcripts. Default: HNRNPC.
 #' @param overlap.tx.gap The gap between transcript groups. Default: 0.1.
-#' @param overlap.style The style of transcript groups, choose from loose (each transcript occupies single line)
-#' and tight (place non-overlap transcripts in one line). Default: loose.
-#' @param tx.size The line size of transcript. Default: 1.
-#' @param utr.size The line size of UTR. Default: 2.
-#' @param exon.size The line size of exon. Default: 3.
-#' @param arrow.size The line size of arrow. Default: 1.5.
+#' @param overlap.style The style of transcript groups, choose from loose (each
+#'   transcript occupies single line) and tight (place non-overlap transcripts
+#'   in one line). Default: loose.
+#' @param tx.size Line size of transcript. Default: 1.
+#' @param utr.size Line size of UTR. Default: 2.
+#' @param exon.size Line size of exon. Default: 3.
+#' @param arrow.angle Angle of the arrow head. Default 35°
+#' @param arrow.length Length of arrows. Default: 1.5
+#' @param arrow.type Whether to draw "closed" or "open" (default) arrow heads
+#' @param color.by Color the line by. Default: strand.
 #' @param arrow.gap The gap distance between intermittent arrows. Default: NULL.
 #'   Set arrow.num and arrow.gap to NULL to suppress intermittent arrows.
-#' @param arrow.num Total number of intermittent arrows over whole region. Default: 50.
-#'   Set arrow.num and arrow.gap to NULL to suppress intermittent arrows.
-#' @param color.by Color the line by. Default: strand.
-#' @param fill.color Color used for \code{color.by}.
-#' Default: blue for - (minus strand), green for + (plus strand).
+#' @param arrow.num Total number of intermittent arrows over whole region.
+#'   Default: 50. Set arrow.num and arrow.gap to NULL to suppress intermittent
+#'   arrows.
+#' @param arrow.size.im Line width of intermittent arrows. Default: 0.5
+#' @param arrow.length.im Length of intermittent arrows. Default: 1.5
+#' @param arrow.type.im Whether to draw "closed" (default) or "open" heads for
+#'   intermittent arrows
+#' @param color.by.im Color the intermittent arrows by variable. Default: NULL
+#'   (draws semi-transparent, white arrows)
+#' @param fill.color Color used for \code{color.by}. Default: blue for - (minus
+#'   strand), green for + (plus strand).
 #' @param label.size The size of transcript label. Default: 3.
 #' @param label.vjust The vjust of transcript label. Default: 2.
 #' @param plot.space Top and bottom margin. Default: 0.1.
-#' @param plot.height The relative height of transcript annotation to coverage plot. Default: 0.2.
+#' @param plot.height The relative height of transcript annotation to coverage
+#'   plot. Default: 0.2.
 #'
 #' @return Plot.
 #' @importFrom dplyr %>%
@@ -30,6 +42,7 @@
 #' @importFrom ggplot2 ggplot_add ggplot geom_segment aes_string arrow unit geom_text labs theme_classic theme element_blank
 #' element_text element_rect margin scale_y_continuous scale_color_manual scale_x_continuous coord_cartesian
 #' @importFrom patchwork wrap_plots
+#' @importFrom grDevices grey
 #' @export
 #'
 #' @examples
@@ -58,9 +71,24 @@
 #' gtf_gr <- rtracklayer::import.gff(con = gtf_file, format = "gtf")
 #'
 #' # plot coverage and gene annotation
-#' basic.coverage <- ggcoverage(data = track_df, range.position = "out")
-#' basic.coverage +
+#' basic_coverage <- ggcoverage(data = track_df, range.position = "out")
+#' basic_coverage +
 #'   geom_transcript(gtf.gr = gtf_gr, label.vjust = 1.5)
+#'
+#' # plot with custom style
+#' basic_coverage +
+#'   geom_transcript(
+#'     gtf.gr = gtf_gr,
+#'     exon.size = 2.0,
+#'     arrow.size.im = 1.0,
+#'     arrow.length.im = 5,
+#'     arrow.type.im = "open",
+#'     color.by.im = "strand",
+#'     fill.color = c(
+#'       "-" = "darkblue",
+#'       "+" = "darkgreen"
+#'     )
+#'   )
 geom_transcript <-
   function(gtf.gr,
            gene.name = "HNRNPC",
@@ -69,10 +97,16 @@ geom_transcript <-
            tx.size = 1,
            utr.size = 2,
            exon.size = 3,
-           arrow.size = 3,
+           arrow.angle = 35,
+           arrow.length = 1.5,
+           arrow.type = "open",
+           color.by = "strand",
            arrow.gap = NULL,
            arrow.num = 50,
-           color.by = "strand",
+           arrow.size.im = 0.5,
+           arrow.length.im = 1.5,
+           arrow.type.im = "closed",
+           color.by.im = NULL,
            fill.color = c(
              "-" = "cornflowerblue",
              "+" = "darkolivegreen3"
@@ -81,33 +115,37 @@ geom_transcript <-
            label.vjust = 2,
            plot.space = 0.1,
            plot.height = 1) {
-    structure(
-      list(
-        gtf.gr = gtf.gr,
-        gene.name = gene.name,
-        overlap.tx.gap = overlap.tx.gap,
-        overlap.style = overlap.style,
-        tx.size = tx.size,
-        utr.size = utr.size,
-        exon.size = exon.size,
-        arrow.size = arrow.size,
-        arrow.gap = arrow.gap,
-        arrow.num = arrow.num,
-        color.by = color.by,
-        fill.color = fill.color,
-        label.size = label.size,
-        label.vjust = label.vjust,
-        plot.space = plot.space,
-        plot.height = plot.height
-      ),
-      class = "transcript"
-    )
-  }
+  structure(
+    list(
+      gtf.gr = gtf.gr,
+      gene.name = gene.name,
+      overlap.tx.gap = overlap.tx.gap,
+      overlap.style = overlap.style,
+      tx.size = tx.size,
+      utr.size = utr.size,
+      exon.size = exon.size,
+      arrow.angle = arrow.angle,
+      arrow.length = arrow.length,
+      arrow.type = arrow.type,
+      color.by = color.by,
+      arrow.gap = arrow.gap,
+      arrow.num = arrow.num,
+      arrow.size.im = arrow.size.im,
+      arrow.length.im = arrow.length.im,
+      arrow.type.im = arrow.type.im,
+      color.by.im = color.by.im,
+      fill.color = fill.color,
+      label.size = label.size,
+      label.vjust = label.vjust,
+      plot.space = plot.space,
+      plot.height = plot.height
+    ),
+    class = "transcript"
+  )
+}
 
 #' @export
 ggplot_add.transcript <- function(object, plot, object_name) {
-  # get plot data
-  # track.data <- plot$layers[[1]]$data
   # get plot data, plot data should contain bins
   if ("patchwork" %in% class(plot)) {
     track.data <- plot[[1]]$layers[[1]]$data
@@ -135,11 +173,17 @@ ggplot_add.transcript <- function(object, plot, object_name) {
   tx.size <- object$tx.size
   utr.size <- object$utr.size
   exon.size <- object$exon.size
-  arrow.size <- object$arrow.size
+  arrow.angle <- object$arrow.angle
+  arrow.length <- object$arrow.length
+  arrow.type <- object$arrow.type
   color.by <- object$color.by
-  fill.color <- object$fill.color
   arrow.gap <- object$arrow.gap
   arrow.num <- object$arrow.num
+  arrow.size.im <- object$arrow.size.im
+  arrow.length.im <- object$arrow.length.im
+  arrow.type.im <- object$arrow.type.im
+  color.by.im <- object$color.by.im
+  fill.color <- object$fill.color
   label.size <- object$label.size
   label.vjust <- object$label.vjust
   plot.space <- object$plot.space
@@ -202,17 +246,17 @@ ggplot_add.transcript <- function(object, plot, object_name) {
 
   # create basic plot
   tx.plot <- ggplot() +
-    geom_arrows(gene.tx.df.tx, color.by, tx.size, arrow.size)
+    geom_arrows(gene.tx.df.tx, color.by, tx.size, arrow.length, arrow.angle, arrow.type)
 
   # deal with missing UTR
   if (is.null(gene.tx.df.utr)) {
     warning("No UTR detected in provided GTF!")
   } else {
     tx.plot <- tx.plot +
-      geom_arrows(gene.tx.df.utr, color.by, utr.size, arrow.size)
+      geom_arrows(gene.tx.df.utr, color.by, utr.size, arrow.length, arrow.angle, arrow.type)
   }
   tx.plot <- tx.plot +
-    geom_arrows(gene.tx.df.exon, color.by, exon.size, arrow.size) +
+    geom_arrows(gene.tx.df.exon, color.by, exon.size, arrow.length, arrow.angle, arrow.type) +
     theme_classic()
 
   if (is.null(arrow.gap)) {
@@ -258,9 +302,22 @@ ggplot_add.transcript <- function(object, plot, object_name) {
   arrow.df$start <- as.numeric(arrow.df$start)
   arrow.df$end <- as.numeric(arrow.df$end)
   arrow.df$group <- as.numeric(arrow.df$group)
+  if (is.null(color.by.im)) {
+    color.by.im <- color.by
+    arrow.df[[color.by]] <- "im"
+    fill.color["im"] <- grDevices::grey(1, alpha = 0.5)
+  } else if (color.by.im %in% colnames(arrow.df)) {
+    stopifnot(unique(arrow.df[[color.by.im]]) %in% names(fill.color))
+  } else {
+    stop(paste0(
+      "The selected variable '",
+      color.by.im ,
+      "' for 'color.by.im' is not available in the data"
+    ))
+  }
   # add arrow
   tx.arrow.plot <- tx.plot +
-    geom_arrows(arrow.df, color.by, tx.size / 2, arrow.size, 35, TRUE)
+    geom_arrows(arrow.df, color.by.im, arrow.size.im, arrow.length.im, arrow.angle, arrow.type.im)
 
   # prepare label dataframe
   label.df <- data.frame(
diff --git a/R/utils.R b/R/utils.R
index 9a755cd..e298989 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -357,7 +357,6 @@ GetPlotData <- function(plot, layer.num = 1) {
 #' @param arrow_size size of the arrow
 #' @param arrow_angle angle of the arrow in degrees
 #' @param arrow_type type of arrow, either 'open' or 'closed'
-#' @importFrom grDevices grey
 #' @return A geom layer for ggplot2 objects.
 #' @export
 geom_arrows <-
diff --git a/man/geom_arrows.Rd b/man/geom_arrows.Rd
index bb1db5d..0d357fe 100644
--- a/man/geom_arrows.Rd
+++ b/man/geom_arrows.Rd
@@ -4,14 +4,7 @@
 \alias{geom_arrows}
 \title{Plot genomic features as arrows.}
 \usage{
-geom_arrows(
-  data,
-  color,
-  line_width,
-  arrow_size,
-  arrow_angle = 35,
-  intermittent = FALSE
-)
+geom_arrows(data, color, line_width, arrow_size, arrow_angle, arrow_type)
 }
 \arguments{
 \item{data}{data frame describing arrow position, with columns
@@ -23,10 +16,9 @@ start, end, group, and a custom 'color' column}
 
 \item{arrow_size}{size of the arrow}
 
-\item{arrow_angle}{angle of the arrow. Default: 35°}
+\item{arrow_angle}{angle of the arrow in degrees}
 
-\item{intermittent}{If TRUE, arrows are only drawn intermittently in
-half-transparent white color. Default: FALSE.}
+\item{arrow_type}{type of arrow, either 'open' or 'closed'}
 }
 \value{
 A geom layer for ggplot2 objects.
diff --git a/man/geom_gene.Rd b/man/geom_gene.Rd
index 6664129..79c5495 100644
--- a/man/geom_gene.Rd
+++ b/man/geom_gene.Rd
@@ -11,10 +11,16 @@ geom_gene(
   gene.size = 1,
   utr.size = 2,
   exon.size = 3,
-  arrow.size = 1.5,
+  arrow.angle = 35,
+  arrow.length = 1.5,
+  arrow.type = "open",
+  color.by = "strand",
   arrow.gap = NULL,
   arrow.num = 50,
-  color.by = "strand",
+  arrow.size.im = 0.5,
+  arrow.length.im = 1.5,
+  arrow.type.im = "closed",
+  color.by.im = NULL,
   fill.color = c(`-` = "cornflowerblue", `+` = "darkolivegreen3"),
   show.utr = FALSE,
   label.size = 3,
@@ -24,28 +30,45 @@ geom_gene(
 )
 }
 \arguments{
-\item{gtf.gr}{Granges object of GTF, created with \code{\link{import.gff}}. Default: NULL.}
+\item{gtf.gr}{Granges object of GTF, created with \code{\link{import.gff}}.
+Default: NULL.}
 
 \item{overlap.gene.gap}{The gap between gene groups. Default: 0.1.}
 
-\item{overlap.style}{The style of gene groups, choose from loose (each gene occupies single line)
-and tight (place non-overlap genes in one line). Default: loose.}
+\item{overlap.style}{The style of gene groups, choose from loose (each gene
+occupies single line) and tight (place non-overlap genes in one line).
+Default: loose.}
+
+\item{gene.size}{Line width of genes. Default: 1.}
+
+\item{utr.size}{Line width of UTRs. Default: 2.}
+
+\item{exon.size}{Line width of exons. Default: 3.}
 
-\item{gene.size}{The line size of gene. Default: 1.}
+\item{arrow.angle}{Angle of the arrow head. Default 35°}
 
-\item{utr.size}{The line size of UTR. Default: 2.}
+\item{arrow.length}{Length of arrows. Default: 1.5}
 
-\item{exon.size}{The line size of exon. Default: 3.}
+\item{arrow.type}{Whether to draw "closed" or "open" (default) arrow heads}
 
-\item{arrow.size}{The line size of arrow. Default: 1.5.}
+\item{color.by}{Color the lines/arrows by variable. Default: "strand".}
 
 \item{arrow.gap}{The gap distance between intermittent arrows. Default: NULL.
 Set arrow.num and arrow.gap to NULL to suppress intermittent arrows.}
 
-\item{arrow.num}{Total number of intermittent arrows over whole region. Default: 50.
-Set arrow.num and arrow.gap to NULL to suppress intermittent arrows.}
+\item{arrow.num}{Total number of intermittent arrows over whole region.
+Default: 50. Set arrow.num and arrow.gap to NULL to suppress intermittent
+arrows.}
+
+\item{arrow.size.im}{Line width of intermittent arrows. Default: 0.5}
+
+\item{arrow.length.im}{Length of intermittent arrows. Default: 1.5}
 
-\item{color.by}{Color the line by. Default: strand.}
+\item{arrow.type.im}{Whether to draw "closed" (default) or "open" heads for
+intermittent arrows}
+
+\item{color.by.im}{Color the intermittent arrows by variable. Default: NULL
+(draws semi-transparent, white arrows)}
 
 \item{fill.color}{Color used for \code{color.by}.
 Default: blue for - (minus strand), green for + (plus strand).}
@@ -58,7 +81,8 @@ Default: blue for - (minus strand), green for + (plus strand).}
 
 \item{plot.space}{Top and bottom margin. Default: 0.1.}
 
-\item{plot.height}{The relative height of gene annotation to coverage plot. Default: 0.2.}
+\item{plot.height}{The relative height of gene annotation to coverage plot.
+Default: 0.2.}
 }
 \value{
 Plot.
@@ -92,7 +116,22 @@ gtf_file <- system.file("extdata", "used_hg19.gtf", package = "ggcoverage")
 gtf_gr <- rtracklayer::import.gff(con = gtf_file, format = "gtf")
 
 # plot coverage and gene annotation
-basic.coverage <- ggcoverage(data = track_df, range.position = "out")
-basic.coverage +
+basic_coverage <- ggcoverage(data = track_df, range.position = "out")
+basic_coverage +
   geom_gene(gtf.gr = gtf_gr)
+
+# plot with custom style
+basic_coverage +
+  geom_gene(
+    gtf.gr = gtf_gr,
+    exon.size = 2.0,
+    arrow.size.im = 1.0,
+    arrow.length.im = 5,
+    arrow.type.im = "open",
+    color.by.im = "strand",
+    fill.color = c(
+      "-" = "darkblue",
+      "+" = "darkgreen"
+    )
+  )
 }
diff --git a/man/geom_transcript.Rd b/man/geom_transcript.Rd
index a2fb109..f2d8be6 100644
--- a/man/geom_transcript.Rd
+++ b/man/geom_transcript.Rd
@@ -12,10 +12,16 @@ geom_transcript(
   tx.size = 1,
   utr.size = 2,
   exon.size = 3,
-  arrow.size = 3,
+  arrow.angle = 35,
+  arrow.length = 1.5,
+  arrow.type = "open",
+  color.by = "strand",
   arrow.gap = NULL,
   arrow.num = 50,
-  color.by = "strand",
+  arrow.size.im = 0.5,
+  arrow.length.im = 1.5,
+  arrow.type.im = "closed",
+  color.by.im = NULL,
   fill.color = c(`-` = "cornflowerblue", `+` = "darkolivegreen3"),
   label.size = 3,
   label.vjust = 2,
@@ -24,33 +30,50 @@ geom_transcript(
 )
 }
 \arguments{
-\item{gtf.gr}{Granges object of GTF, created with \code{\link{import.gff}}. Default: NULL.}
+\item{gtf.gr}{Granges object of GTF, created with \code{\link{import.gff}}.
+Default: NULL.}
 
 \item{gene.name}{Gene name of all transcripts. Default: HNRNPC.}
 
 \item{overlap.tx.gap}{The gap between transcript groups. Default: 0.1.}
 
-\item{overlap.style}{The style of transcript groups, choose from loose (each transcript occupies single line)
-and tight (place non-overlap transcripts in one line). Default: loose.}
+\item{overlap.style}{The style of transcript groups, choose from loose (each
+transcript occupies single line) and tight (place non-overlap transcripts
+in one line). Default: loose.}
+
+\item{tx.size}{Line size of transcript. Default: 1.}
 
-\item{tx.size}{The line size of transcript. Default: 1.}
+\item{utr.size}{Line size of UTR. Default: 2.}
 
-\item{utr.size}{The line size of UTR. Default: 2.}
+\item{exon.size}{Line size of exon. Default: 3.}
 
-\item{exon.size}{The line size of exon. Default: 3.}
+\item{arrow.angle}{Angle of the arrow head. Default 35°}
 
-\item{arrow.size}{The line size of arrow. Default: 1.5.}
+\item{arrow.length}{Length of arrows. Default: 1.5}
+
+\item{arrow.type}{Whether to draw "closed" or "open" (default) arrow heads}
+
+\item{color.by}{Color the line by. Default: strand.}
 
 \item{arrow.gap}{The gap distance between intermittent arrows. Default: NULL.
 Set arrow.num and arrow.gap to NULL to suppress intermittent arrows.}
 
-\item{arrow.num}{Total number of intermittent arrows over whole region. Default: 50.
-Set arrow.num and arrow.gap to NULL to suppress intermittent arrows.}
+\item{arrow.num}{Total number of intermittent arrows over whole region.
+Default: 50. Set arrow.num and arrow.gap to NULL to suppress intermittent
+arrows.}
 
-\item{color.by}{Color the line by. Default: strand.}
+\item{arrow.size.im}{Line width of intermittent arrows. Default: 0.5}
+
+\item{arrow.length.im}{Length of intermittent arrows. Default: 1.5}
 
-\item{fill.color}{Color used for \code{color.by}.
-Default: blue for - (minus strand), green for + (plus strand).}
+\item{arrow.type.im}{Whether to draw "closed" (default) or "open" heads for
+intermittent arrows}
+
+\item{color.by.im}{Color the intermittent arrows by variable. Default: NULL
+(draws semi-transparent, white arrows)}
+
+\item{fill.color}{Color used for \code{color.by}. Default: blue for - (minus
+strand), green for + (plus strand).}
 
 \item{label.size}{The size of transcript label. Default: 3.}
 
@@ -58,7 +81,8 @@ Default: blue for - (minus strand), green for + (plus strand).}
 
 \item{plot.space}{Top and bottom margin. Default: 0.1.}
 
-\item{plot.height}{The relative height of transcript annotation to coverage plot. Default: 0.2.}
+\item{plot.height}{The relative height of transcript annotation to coverage
+plot. Default: 0.2.}
 }
 \value{
 Plot.
@@ -92,7 +116,22 @@ gtf_file <- system.file("extdata", "used_hg19.gtf", package = "ggcoverage")
 gtf_gr <- rtracklayer::import.gff(con = gtf_file, format = "gtf")
 
 # plot coverage and gene annotation
-basic.coverage <- ggcoverage(data = track_df, range.position = "out")
-basic.coverage +
+basic_coverage <- ggcoverage(data = track_df, range.position = "out")
+basic_coverage +
   geom_transcript(gtf.gr = gtf_gr, label.vjust = 1.5)
+
+# plot with custom style
+basic_coverage +
+  geom_transcript(
+    gtf.gr = gtf_gr,
+    exon.size = 2.0,
+    arrow.size.im = 1.0,
+    arrow.length.im = 5,
+    arrow.type.im = "open",
+    color.by.im = "strand",
+    fill.color = c(
+      "-" = "darkblue",
+      "+" = "darkgreen"
+    )
+  )
 }

From e146f3db23161e280bb049687d028688e0558b21 Mon Sep 17 00:00:00 2001
From: jahn <jahn@mpusp.mpg.de>
Date: Wed, 23 Oct 2024 14:55:57 +0200
Subject: [PATCH 5/6] fix: mark region boundaries, closes #39

---
 R/geom_coverage.R | 32 +++++++++++---------------------
 1 file changed, 11 insertions(+), 21 deletions(-)

diff --git a/R/geom_coverage.R b/R/geom_coverage.R
index 2556a43..2a54f7c 100644
--- a/R/geom_coverage.R
+++ b/R/geom_coverage.R
@@ -31,7 +31,7 @@
 #' @importFrom stats as.formula
 #' @importFrom ggh4x facet_wrap2 strip_themed elem_list_rect
 #' @importFrom dplyr group_by summarise
-#' @importFrom dplyr %>%
+#' @importFrom dplyr %>% filter
 #' @importFrom ggrepel geom_text_repel
 #' @importFrom utils tail
 #'
@@ -336,34 +336,24 @@ geom_coverage <- function(data, mapping = NULL, color = NULL, rect.color = NA,
   # add rect
   if (!is.null(mark.region)) {
     # get valid mark region
-    region.start <- data[1, "start"]
-    region.end <- data[nrow(data), "end"]
-    valid.region.list <- list()
-    for (r in 1:nrow(mark.region)) {
-      if (mark.region[r, "start"] <= region.end & mark.region[r, "end"] >= region.start) {
-        if (mark.region[r, "end"] >= region.end) {
-          mark.region[r, "end"] <- region.end
-        }
-        if (mark.region[r, "start"] <= region.start) {
-          mark.region[r, "start"] <- region.start
-        }
-        valid.region.list[[r]] <- mark.region[r, ]
-      }
-    }
-    valid.region.df <- do.call(rbind, valid.region.list) %>% as.data.frame()
-    colnames(valid.region.df) <- colnames(mark.region)
-
+    region.start <- min(data$start)
+    region.end <- max(data$end)
+    mark.region <- dplyr::filter(
+      mark.region,
+      .data[["start"]] >= region.start,
+      .data[["end"]] <= region.end
+    )
     region.mark <- geom_rect(
-      data = valid.region.df,
+      data = mark.region,
       aes_string(xmin = "start", xmax = "end", ymin = "-Inf", ymax = "Inf"),
       fill = mark.color, alpha = mark.alpha
     )
     plot.ele <- append(plot.ele, region.mark)
     # add rect label
     if (show.mark.label) {
-      if ("label" %in% colnames(valid.region.df)) {
+      if ("label" %in% colnames(mark.region)) {
         # create mark region label
-        region.label <- valid.region.df
+        region.label <- mark.region
         if (plot.type == "facet") {
           region.label[, facet.key] <- facet.order[1]
         }

From 1d9174f659ac27572c0e051faf2be7380d901a47 Mon Sep 17 00:00:00 2001
From: jahn <jahn@mpusp.mpg.de>
Date: Fri, 3 Jan 2025 10:49:10 +0100
Subject: [PATCH 6/6] fix: facet order with region labels, closes #40

---
 R/geom_coverage.R | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/R/geom_coverage.R b/R/geom_coverage.R
index 2a54f7c..8203d11 100644
--- a/R/geom_coverage.R
+++ b/R/geom_coverage.R
@@ -355,7 +355,10 @@ geom_coverage <- function(data, mapping = NULL, color = NULL, rect.color = NA,
         # create mark region label
         region.label <- mark.region
         if (plot.type == "facet") {
-          region.label[, facet.key] <- facet.order[1]
+          region.label[, facet.key] <- factor(
+            rep(facet.order[1], nrow(mark.region)),
+            facet.order
+          )
         }
         region.mark.label <- geom_text_repel(
           data = region.label,