remove 'allmuts' and mutation regex columns from ggtree object's data

R/plot_tree.R

@@ -47,10 +47,7 @@ create_trees <- function(ggtree_data,
 
   tree_list$with_interactivity_data <- append_interactivity_data(
     tree_list[["noninteractive"]],
-    branch_col = branch_col,
-    sc0 = sc0,
-    cmuts = cmuts,
-    mut_regex = mut_regex
+    branch_col = branch_col
   )
 
   genotype <- extract_genotype_data(
@@ -187,22 +184,17 @@ create_noninteractive_ggtree <- function(ggtree_data,
   gtr1.1
 }
 
-#' Adds data to a ggtree object to allow mouse-over tooltips etc when presented interactively
+#' Adds data to a \code{ggtree} object to allow mouse-over tooltips etc when presented interactively
 #'
 #' @param   ggobj   A \code{ggtree} object.
 #' @param   branch_col    Scalar string. The name of a column within \code{ggobj$data} defining the
 #'   statistic under study here (`logistic_growth_rate`, `clock_outlier`).
-#' @inheritParams   create_trees
 #'
-#' @return  A ggtree object. The \code{$data} entry has additional entries (\code{mouseover},
-#'   \code{colour_var}, \code{allmuts}) that are used when presented interactively by
-#'   \code{ggiraph}.
+#' @return  A \code{ggtree} object. The \code{$data} entry has additional entries (\code{mouseover},
+#'   \code{colour_var}) that are used when presented interactively by \code{ggiraph}.
 
 append_interactivity_data <- function(ggobj,
-                                      branch_col,
-                                      sc0,
-                                      cmuts,
-                                      mut_regex) {
+                                      branch_col) {
   # make mouseover info
   ## standard meta data
   ttdfs <- apply(ggobj$data, 1, FUN = function(x) {
@@ -218,36 +210,6 @@ append_interactivity_data <- function(ggobj,
     )
   })
 
-  ttallmuts <- sapply(match(ggobj$data$cluster_id, sc0$cluster_id), function(isc0) {
-    if (is.na(isc0)) {
-      return("")
-    }
-    paste(
-      sep = "\n",
-      "All mutations:",
-      gsub(
-        x = stringr::str_wrap(
-          paste(
-            collapse = " ",
-            sort_mutations(cmuts[[as.character(sc0$node_number[isc0])]]$all)
-          ),
-          width = 60
-        ),
-        pattern = " ",
-        replacement = ", "
-      ),
-      "\n"
-    )
-  }) # end of sapply
-
-  ggobj$data$allmuts <- ttallmuts
-  if (!is.null(mut_regex)) {
-    for (mre in mut_regex) {
-      i <- which(grepl(ggobj$data$allmuts, pattern = mre))
-      ggobj$data[[mre]] <- grepl(ggobj$data$allmuts, pattern = mre)
-    }
-  }
-
   ggobj$data$mouseover <- ttdfs
   ggobj$data$colour_var <- ggobj$data[[branch_col]]