From 00390dea02e4706e1d2a71052a4e5d4ce0b81913 Mon Sep 17 00:00:00 2001
From: peekxc <matt.piekenbrock@gmail.com>
Date: Thu, 8 Aug 2019 11:05:42 -0400
Subject: [PATCH] Merging edits, fixed implicit namespace imports w/ grDevices

---
 DESCRIPTION             | 3 ++-
 R/simplex_tree.R        | 9 +++++----
 man/plot.simplextree.Rd | 3 ++-
 3 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 08e785f..4082297 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -18,4 +18,5 @@ Suggests:
     testthat, 
     igraph, 
     knitr, 
-    rmarkdown
+    rmarkdown, 
+    viridis
diff --git a/R/simplex_tree.R b/R/simplex_tree.R
index df3f897..400c18f 100644
--- a/R/simplex_tree.R
+++ b/R/simplex_tree.R
@@ -552,7 +552,8 @@ NULL
 #'   coords <- igraph::layout.auto(g)
 #'   
 #'   ## Create rainbow colors 
-#'   si_names <- sapply(st$ltraverse(identity, "bfs"), function(simplex){ paste0(simplex, collapse=",") })[-1]
+#'   si_to_str <- function(simplex) { paste0(simplex, collapse=",") }
+#'   si_names <- sapply(st$ltraverse(identity, "bfs"), si_to_str)[-1]
 #'   si_colors <- structure(as.list(rainbow(sum(st$n_simplices))), names=si_names)
 #'   
 #'   ## Make animation
@@ -573,7 +574,7 @@ plot.Rcpp_SimplexTree <- function (x, coords = NULL, vertex_opt=NULL, text_opt=N
     if (n_colors <= 9){
       color_pal <- .default_st_colors[seq(n_colors)]
     } else {
-      color_pal <- substr(rev(rainbow(n_colors, start=0, end=4/6)), start=1,stop=7)
+      color_pal <- substr(rev(grDevices::rainbow(n_colors, start=0, end=4/6)), start=1,stop=7)
     }
   }
   
@@ -615,7 +616,7 @@ plot.Rcpp_SimplexTree <- function (x, coords = NULL, vertex_opt=NULL, text_opt=N
     is_hex <- substring(color_pal, first=1,last=1) == "#"
     is_rgb <- nchar(color_pal) == 7
     is_col <- (!is_hex | (is_hex && is_rgb))
-    color_pal[is_col] <- apply(col2rgb(color_pal[is_col]), 2, function(col){ do.call(rgb, as.list(col/255)) })
+    color_pal[is_col] <- apply(grDevices::col2rgb(color_pal[is_col]), 2, function(col){ do.call(grDevices::rgb, as.list(col/255)) })
     color_pal[is_col] <- alpha4sc(color_pal)[is_col]
     simplex_colors <- color_pal[dim_idx+1L]
   } else {
@@ -645,7 +646,7 @@ plot.Rcpp_SimplexTree <- function (x, coords = NULL, vertex_opt=NULL, text_opt=N
         polys <- x$ltraverse(empty_face, function(simplex){ 
           # idx <- match(simplex[combn(d+1L, 3L)], v)
           poly <- coords[match(simplex, v),] 
-          rbind(poly[chull(poly),], c(NA, NA))
+          rbind(poly[grDevices::chull(poly),], c(NA, NA))
         }, "maximal-skeleton", list(k=d))
         subset <- (draw_simplex & (dim_idx==d))
         d_subset <- subset[dim_idx==d]
diff --git a/man/plot.simplextree.Rd b/man/plot.simplextree.Rd
index f03d322..d106168 100644
--- a/man/plot.simplextree.Rd
+++ b/man/plot.simplextree.Rd
@@ -118,7 +118,8 @@ plot(st, color_pal=append(blue_vertices, list("5,6,7,8,9"="red")))
   coords <- igraph::layout.auto(g)
   
   ## Create rainbow colors 
-  si_names <- sapply(st$ltraverse(identity, "bfs"), function(simplex){ paste0(simplex, collapse=",") })[-1]
+  si_to_str <- function(simplex) { paste0(simplex, collapse=",") }
+  si_names <- sapply(st$ltraverse(identity, "bfs"), si_to_str)[-1]
   si_colors <- structure(as.list(rainbow(sum(st$n_simplices))), names=si_names)
   
   ## Make animation