Add vignette & bugfix

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SpatialPhyloPlot
 Type: Package
 Title: Automated Plotting of Phylogenetic Trees on Spatial Transcriptomics Data
-Version: 0.3.0
+Version: 0.4.0
 Date: 2025-07-20
 Authors@R: c(
     person(
@@ -16,7 +16,6 @@ Encoding: UTF-8
 LazyData: true
 URL: https://github.com/Wedge-lab/SpatialPhyloPlot
 BugReports: https://github.com/Wedge-lab/SpatialPhyloPlot
-Depends:
 Imports:
     alakazam,
     ape,
@@ -27,6 +26,9 @@ Imports:
     rjson,
     pals
 Suggests: 
+    knitr,
+    rmarkdown,
     testthat
 Config/testthat/edition: 3
 RoxygenNote: 7.3.2
+VignetteBuilder: knitr

R/SpatialPhyloPlot.R

@@ -54,6 +54,8 @@ SpatialPhyloPlot <- function(visium_version,
                              plot_points = TRUE,
                              plot_polygon = FALSE,
                              point_alpha = 0.8,
+                             point_size = 1.5,
+                             point_shape = 19,
                              hull_alpha = 0,
                              hull_expansion = 0.005,
                              centroid_alpha = 0.9,
@@ -551,6 +553,8 @@ SpatialPhyloPlot <- function(visium_version,
     plot_points = plot_points,
     plot_polygon = plot_polygon,
     point_alpha = point_alpha,
+    point_size = point_size,
+    point_shape = point_shape,
     hull_alpha = hull_alpha,
     hull_expansion = hull_expansion,
     centroid_alpha = centroid_alpha,

R/visualisation.R

@@ -69,6 +69,8 @@ img_name_colours <- function(newick_df) {
 #' @param newick_df The newick `data.frame` generated from the .new phylogenetic tree file.
 #' @param from_to_df A `data.frame` containing the start and end coordinates of each branch on the phylogenetic tree.
 #' @param point_alpha The alpha transparency value for points, default is `0.8`.
+#' @param point_size The size of the Visium spot points, default is `1.5`.
+#' @param point_shape The shape to use for the Visium spot points, default is `19`.
 #' @param hull_alpha The alpha transparency value for polygons/hulls to be plotted, default is `0` (not plotted).
 #' @param hull_expansion The hull/polygon extension amount, default is `0.005`.
 #' @param centroid_alpha The alpha transparency value for the centroids plotted as part of the phylogenetic tree, default is `0.9`.
@@ -136,6 +138,8 @@ img_plot <- function(raster_img,
                      plot_points = TRUE,
                      plot_polygon = FALSE,
                      point_alpha = 0.8,
+                     point_size = 1.5,
+                     point_shape = 19,
                      hull_alpha = 0,
                      hull_expansion = 0.005,
                      centroid_alpha = 0.9,
@@ -203,28 +207,28 @@ img_plot <- function(raster_img,
   if(plot_points){
     p <- p +
       geom_point(data = coordinates_df_scaled, aes(x = new_x_scaled, y = new_y_scaled, colour = Clone),
-                 alpha = point_alpha, show.legend = NA)
+                 alpha = point_alpha, show.legend = NA, size = point_size, shape = point_shape)
     # plotting multisample points
     if(multisample & shared_clones){
       if(!all(is.na(coordinates_df_scaled_left))){
         p <- p +
           geom_point(data = coordinates_df_scaled_left, aes(x = new_x_scaled, y = new_y_scaled, colour = Clone),
-                     alpha = point_alpha, show.legend = NA)
+                     alpha = point_alpha, show.legend = NA, size = point_size, shape = point_shape)
       }
       if(!all(is.na(coordinates_df_scaled_right))){
         p <- p +
           geom_point(data = coordinates_df_scaled_right, aes(x = new_x_scaled, y = new_y_scaled, colour = Clone),
-                     alpha = point_alpha, show.legend = NA)
+                     alpha = point_alpha, show.legend = NA, size = point_size, shape = point_shape)
       }
       if(!all(is.na(coordinates_df_scaled_top))){
         p <- p +
           geom_point(data = coordinates_df_scaled_top, aes(x = new_x_scaled, y = new_y_scaled, colour = Clone),
-                     alpha = point_alpha, show.legend = NA)
+                     alpha = point_alpha, show.legend = NA, size = point_size, shape = point_shape)
       }
       if(!all(is.na(coordinates_df_scaled_bottom))){
         p <- p +
           geom_point(data = coordinates_df_scaled_bottom, aes(x = new_x_scaled, y = new_y_scaled, colour = Clone),
-                     alpha = point_alpha, show.legend = NA)
+                     alpha = point_alpha, show.legend = NA, size = point_size, shape = point_shape)
       }
     }
   }
@@ -319,28 +323,28 @@ img_plot <- function(raster_img,
   if(plot_internal_nodes){
     p <- p +
       geom_point(data = subset(newick_df, is.na(colour)), aes(x = centroid_x, y = centroid_y, colour = "Internal Node", fill = internal_node_colour),
-                 size = internal_node_size, alpha = internal_node_alpha, show.legend = NA, shape = 21, colour = internal_node_colour)
+                 size = internal_node_size, alpha = internal_node_alpha, show.legend = NA, shape = 21, fill = internal_node_colour)
 
     if(multisample & shared_clones){
       if(!all(is.na(newick_df_left))){
         p <- p +
           geom_point(data = subset(newick_df_left, is.na(colour)), aes(x = centroid_x, y = centroid_y, colour = "Internal Node", fill = internal_node_colour),
-                     size = internal_node_size, alpha = internal_node_alpha, show.legend = NA, shape = 21, colour = internal_node_colour)
+                     size = internal_node_size, alpha = internal_node_alpha, show.legend = NA, shape = 21, fill = internal_node_colour)
       }
       if(!all(is.na(newick_df_right))){
         p <- p +
           geom_point(data = subset(newick_df_right, is.na(colour)), aes(x = centroid_x, y = centroid_y, colour = "Internal Node", fill = internal_node_colour),
-                     size = internal_node_size, alpha = internal_node_alpha, show.legend = NA, shape = 21, colour = internal_node_colour)
+                     size = internal_node_size, alpha = internal_node_alpha, show.legend = NA, shape = 21, fill = internal_node_colour)
       }
       if(!all(is.na(newick_df_top))){
         p <- p +
           geom_point(data = subset(newick_df_top, is.na(colour)), aes(x = centroid_x, y = centroid_y, colour = "Internal Node", fill = internal_node_colour),
-                     size = internal_node_size, alpha = internal_node_alpha, show.legend = NA, shape = 21, colour = internal_node_colour)
+                     size = internal_node_size, alpha = internal_node_alpha, show.legend = NA, shape = 21, fill = internal_node_colour)
       }
       if(!all(is.na(newick_df_bottom))){
         p <- p +
           geom_point(data = subset(newick_df_bottom, is.na(colour)), aes(x = centroid_x, y = centroid_y, colour = "Internal Node", fill = internal_node_colour),
-                     size = internal_node_size, alpha = internal_node_alpha, show.legend = NA, shape = 21, colour = internal_node_colour)
+                     size = internal_node_size, alpha = internal_node_alpha, show.legend = NA, shape = 21, fill = internal_node_colour)
       }
     }
   }