From 104aa63d442ba663500a018ac1fb6c53dd5461ce Mon Sep 17 00:00:00 2001
From: Martin Petr <git@bodkan.net>
Date: Wed, 21 Jun 2023 09:22:23 +0200
Subject: [PATCH] Add option not to draw gene-flow arrows

---
 R/visualization.R |  5 +++--
 man/plot_model.Rd | 10 +++++++++-
 2 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/R/visualization.R b/R/visualization.R
index 984b2bc94..283295355 100644
--- a/R/visualization.R
+++ b/R/visualization.R
@@ -256,6 +256,7 @@ sort_splits <- function(model) {
 #' @param sizes Should population size changes be visualized?
 #' @param proportions Should gene flow proportions be visualized (\code{FALSE}
 #'   by default to prevent cluttering and overplotting)
+#' @param gene_flow Should gene-flow arrows be visualized (default \code{TRUE}).
 #' @param log Should the y-axis be plotted on a log scale? Useful for models
 #'   over very long time-scales.
 #'
@@ -275,7 +276,7 @@ sort_splits <- function(model) {
 #'   geom_polygon geom_label scale_y_continuous scale_color_discrete scale_fill_discrete
 #'   labs geom_segment arrow
 #' @export
-plot_model <- function(model, sizes = TRUE, proportions = FALSE, log = FALSE) {
+plot_model <- function(model, sizes = TRUE, proportions = FALSE, gene_flow = TRUE, log = FALSE) {
   populations <- model$populations
 
   log10_ydelta <- 0.001
@@ -415,7 +416,7 @@ plot_model <- function(model, sizes = TRUE, proportions = FALSE, log = FALSE) {
 
   # generate a table of gene flow events to be used for plotting gene flow
   # arrows
-  if (!is.null(model$geneflow)) {
+  if (!is.null(model$geneflow) && gene_flow) {
     gene_flow <- model$geneflow %>%
       dplyr::mutate(
         x = purrr::map_dbl(from, ~ centers[centers$pop == .x, ]$center),
diff --git a/man/plot_model.Rd b/man/plot_model.Rd
index 7cb298b7c..a7d96762f 100644
--- a/man/plot_model.Rd
+++ b/man/plot_model.Rd
@@ -4,7 +4,13 @@
 \alias{plot_model}
 \title{Plot demographic history encoded in a slendr model}
 \usage{
-plot_model(model, sizes = TRUE, proportions = FALSE, log = FALSE)
+plot_model(
+  model,
+  sizes = TRUE,
+  proportions = FALSE,
+  gene_flow = TRUE,
+  log = FALSE
+)
 }
 \arguments{
 \item{model}{Compiled \code{slendr_model} model object}
@@ -14,6 +20,8 @@ plot_model(model, sizes = TRUE, proportions = FALSE, log = FALSE)
 \item{proportions}{Should gene flow proportions be visualized (\code{FALSE}
 by default to prevent cluttering and overplotting)}
 
+\item{gene_flow}{Should gene-flow arrows be visualized (default \code{TRUE}).}
+
 \item{log}{Should the y-axis be plotted on a log scale? Useful for models
 over very long time-scales.}
 }