Create plotTree.R

noriakis · Sep 1, 2023 · c5cb621 · c5cb621
1 parent 40b7016
commit c5cb621
Showing 1 changed file with 23 additions and 0 deletions.
diff --git a/R/plotTree.R b/R/plotTree.R
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+#' plotTree
+#' 
+#' infer the tree and plot
+#' 
+#' @param stana
+#' @param species
+#' 
+#' @export
+plotTree <- function(stana, species, cl=NULL) {
+	if (is.null(cl)) {cl <- stana@cl}
+	tre <- stana@fastaList[[species]]
+	dm <- dist.ml(tre, "F81")
+	tre <- NJ(dm)
+	stana@treeList[[species]] <- tre
+    tre <- groupOTU(tre, cl)
+    tp <- ggtree(tre,
+        layout='circular',branch.length = "none") + # Return cladogram by default
+        geom_tippoint(size=3, aes(color=.data$group)) +
+        ggtitle(species)+
+        scale_color_manual(values=stana@colors)
+    stana@treePlotList[[species]] <- tp
+    stana
+}