Merge pull request #147 from uclahs-cds/hwinata-add-polygon-parameters

add polygon params

NEWS.md

@@ -7,6 +7,7 @@
 * Documentation for heatmaps and clone-genome distribution plot
 * Option to disable node drawing with node-by-node control
 * Node-by-node control of node size
+* Add parameters to specify polygon shape and width.
 
 ## Update
 * Fixed angle calculation bug where child angles do not follow

R/SRCGrob.R

@@ -22,9 +22,10 @@ SRCGrob <- function(
     add.normal = FALSE,
     use.radians = FALSE,
     normal.cex = 1,
-    sig.shape = 3,
     label.nodes = TRUE,
     disable.polygons = FALSE,
+    polygon.shape = 3,
+    polygon.width = 1.2,
     length.from.node.edge = TRUE,
     size.units = 'npc'
     ) {
@@ -49,7 +50,6 @@ SRCGrob <- function(
 
     fixed.angle <- pi / 6;
     min.width <- get.plot.width(horizontal.padding);
-    wid <- 1.2;
     spread <- 1;
     cluster.list <- NULL;
     node.radius <- 0.1;
@@ -80,11 +80,11 @@ SRCGrob <- function(
         scale1 = scale1,
         scale2 = scale2,
         yat = yat,
-        wid = wid,
+        wid = polygon.width,
         length.from.node.edge = length.from.node.edge,
         default.branch.width = 4,
         add.polygons = add.polygons,
-        sig.shape = sig.shape,
+        sig.shape = polygon.shape,
         spread = spread,
         fixed.angle = fixed.angle,
         add.node.text = add.node.text,

man/SRCGrob.Rd

@@ -30,9 +30,10 @@ SRCGrob(
     add.normal = FALSE,
     use.radians = FALSE,
     normal.cex = 1,
-    sig.shape = 3,
     label.nodes = TRUE,
     disable.polygons = FALSE,
+    polygon.shape = 3,
+    polygon.width = 1.2,
     length.from.node.edge = TRUE,
     size.units = "npc"
     );
@@ -73,12 +74,13 @@ SRCGrob(
   \item{add.normal}{Adds a normal}
   \item{use.radians}{Unit to be used for "angle" column (degrees or radians)}
   \item{normal.cex}{Font size within the normal "box"}
-  \item{sig.shape}{
+  \item{label.nodes}{Enable/disable node labels}
+  \item{disable.polygons}{Disables CP polygon drawing (even when CP values are provided)}
+  \item{polygon.shape}{
   Changes the shape of the CP shading.
   Lower values are smoother.
   }
-  \item{label.nodes}{Enable/disable node labels}
-  \item{disable.polygons}{Disables CP polygon drawing (even when CP values are provided)}
+\item{polygon.width}{Width of the CP shading}
   \item{length.from.node.edge}{
   Sets the branch length to be calculated from the edge of the node instead of the centre
   }