fix: colour issues (#146)

Added new `edge_alpha` argument and flipped default colour scheme from black to white.

R/network_p2p.R

@@ -48,7 +48,9 @@
 #' @param palette Function for generating a colour palette with a single
 #'   argument `n`. Uses "rainbow" by default.
 #' @param node_alpha A numeric value between 0 and 1 to specify the transparency
-#'   of the nodes.
+#'   of the nodes. Defaults to 0.7.
+#' @param edge_alpha A numeric value between 0 and 1 to specify the transparency
+#'   of the edges (only for 'ggraph' mode). Defaults to 1.
 #' @param res Resolution parameter to be passed to `leiden::leiden()`. Defaults
 #'   to 0.5.
 #' @param seed Seed for the random number generator passed to `leiden::leiden()`
@@ -144,11 +146,12 @@ network_p2p <- function(data,
                         return = "plot",
                         path = paste0("network_p2p_", display),
                         desc_hrvar = c("Organization", "LevelDesignation", "FunctionType"),
-                        bg_fill = "#000000",
-                        font_col = "#FFFFFF",
+                        bg_fill = "#FFFFFF",
+                        font_col = "grey20",
                         legend_pos = "bottom",
                         palette = "rainbow",
                         node_alpha = 0.7,
+                        edge_alpha = 1,
                         res = 0.5,
                         seed = 1,
                         algorithm = "mds",
@@ -337,7 +340,7 @@ network_p2p <- function(data,
 
       plot_output <-
         g_layout +
-        ggraph::geom_edge_link(colour = "lightgrey", edge_width = 0.05, alpha = 0.15) +
+        ggraph::geom_edge_link(colour = "lightgrey", edge_width = 0.05, alpha = edge_alpha) +
         ggraph::geom_node_point(aes(colour = !!sym(v_attr)),
                                 alpha = node_alpha,
                                 pch = 16) +

man/network_leiden.Rd

@@ -39,7 +39,7 @@ list of options.}
 path based on current parameters.}
 
 \item{node_alpha}{A numeric value between 0 and 1 to specify the transparency
-of the nodes.}
+of the nodes. Defaults to 0.7.}
 
 \item{res}{Resolution parameter to be passed to \code{leiden::leiden()}. Defaults
 to 0.5.}

man/network_louvain.Rd

@@ -28,7 +28,7 @@ network_louvain(
 \item{font_col}{String to specify font and link colour.}
 
 \item{node_alpha}{A numeric value between 0 and 1 to specify the transparency
-of the nodes.}
+of the nodes. Defaults to 0.7.}
 
 \item{algorithm}{String to specify the node placement algorithm to be used.
 Defaults to \code{"mds"} for the deterministic multi-dimensional scaling of

man/network_p2p.Rd

@@ -11,11 +11,12 @@ network_p2p(
   return = "plot",
   path = paste0("network_p2p_", display),
   desc_hrvar = c("Organization", "LevelDesignation", "FunctionType"),
-  bg_fill = "#000000",
-  font_col = "#FFFFFF",
+  bg_fill = "#FFFFFF",
+  font_col = "grey20",
   legend_pos = "bottom",
   palette = "rainbow",
   node_alpha = 0.7,
+  edge_alpha = 1,
   res = 0.5,
   seed = 1,
   algorithm = "mds",
@@ -70,7 +71,10 @@ the 'ggraph' plotting method is being used.}
 argument \code{n}. Uses "rainbow" by default.}
 
 \item{node_alpha}{A numeric value between 0 and 1 to specify the transparency
-of the nodes.}
+of the nodes. Defaults to 0.7.}
+
+\item{edge_alpha}{A numeric value between 0 and 1 to specify the transparency
+of the edges (only for 'ggraph' mode). Defaults to 1.}
 
 \item{res}{Resolution parameter to be passed to \code{leiden::leiden()}. Defaults
 to 0.5.}