diff --git a/DESCRIPTION b/DESCRIPTION
index e48a997..585c84a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: CancerEvolutionVisualization
 Title: Publication Quality Phylogenetic Tree Plots
-Version: 2.1.1
-Date: 2024-07-30
+Version: 2.1.0
+Date: 2024-07-31
 Authors@R: c(
 	person("Paul Boutros", role = "cre", email = "PBoutros@mednet.ucla.edu"),
 	person("Adriana Salcedo", role = "aut"),
@@ -19,10 +19,8 @@ Depends:
 	gridExtra,
 	gtable,
 Imports:
-    plyr,
     grDevices,
     utils,
-    stringr,
     BoutrosLab.plotting.general
 Suggests:
     testthat,
diff --git a/NAMESPACE b/NAMESPACE
index 51d41bd..c8e9d06 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,13 +1,11 @@
 import(grid)
 import(gridExtra)
 import(gtable)
-import(plyr)
 import(BoutrosLab.plotting.general)
 
 importFrom("graphics", "par", "strheight", "strwidth")
 importFrom("grDevices", "dev.list", "rainbow")
 importFrom("utils", "read.table", "vi", "head")
-importFrom("stringr", "str_replace_all")
 importFrom("stats", "setNames", "aggregate", "reshape")
 importFrom("grDevices", "col2rgb")
 
diff --git a/NEWS.md b/NEWS.md
index 478a582..9d9b4a9 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# CancerEvolutionVisualization 2.1.0 (2024-07-30)
+# CancerEvolutionVisualization 2.1.0 (2024-07-31)
 
 ## Added
 * Optional "spread" column to control node/branch spacing
@@ -9,8 +9,14 @@
 * Fixed angle calculation bug where child angles do not follow
   their parent angle, instead moving "downward" at 0 degrees.
 * Updated package metadata and README
+<<<<<<< HEAD:NEWS.md
 * Set default parameters for heatmaps, defaulting too BPG defaults unless necessary
 * Updated changelog format to NEWS.md Markdown format
+=======
+* Refactored use of plyr/dplyr and stringr functions to remove dependencies
+* Set default parameters for heatmaps, defaulting to BPG defaults unless necessary
+
+>>>>>>> 2424b7934e815dcc02cce5482c1b1c16bf319a09:NEWS
 
 
 # CancerEvolutionVisualization 2.0.1 (2023-11-17)
diff --git a/R/add.segs.R b/R/add.segs.R
index a4fc155..eab529f 100644
--- a/R/add.segs.R
+++ b/R/add.segs.R
@@ -1,99 +1,3 @@
-add.segs3 <- function(
-    tree,
-    v,
-    offset = 0,
-    node.radius = 0,
-    scale.x.real = NULL
-    ) {
-
-    # Calculate offset based on line width
-    offset <- offset / scale.x.real / 2;
-
-    tree.segs.adjusted <- tree.segs <- adply(
-        tree,
-        .margins = 1,
-        .fun = function(x) {
-            if (x$parent == -1) {
-                basey <- 0;
-                basex <- 0;
-            } else {
-                basey <- v$y[v$id == x$parent];
-                basex <- v$x[v$id == x$parent];
-                }
-
-            tipy <- basey + x$length1 * cos(x$angle);
-            tipx <- basex + x$length1 * sin(x$angle);
-
-            return(data.frame(basex, basey, tipx, tipy));
-            }
-        );
-
-    tree.out <- list();
-
-    second.tree.segs.adjusted <- NULL;
-
-    if (length(grep('length', colnames(tree))) == 4) {
-        tree.segs.adjusted <- adply(
-            tree.segs,
-            .margins = 1,
-            .fun = function(r) {
-                offset.x <- offset * cos(r$angle);
-                offset.y <- offset * sin(r$angle);
-
-                if (r$angle > 0) {
-                    basey <- r$basey + offset.y;
-                    tipy <- r$tipy + offset.y;
-                } else {
-                    basey <- r$basey + offset.y;
-                    tipy <- r$tipy + offset.y;
-                    }
-
-                basex <- r$basex - offset.x;
-                tipx <- r$tipx - offset.x;
-
-                return(data.frame(basex, basey, tipx, tipy));
-                }
-            );
-
-        tree.segs.adjusted <- tree.segs.adjusted[which(!(tree.segs.adjusted$basey == tree.segs.adjusted$tipy & tree.segs.adjusted$basex == tree.segs.adjusted$tipx)), ]
-
-        second.tree.segs <- tree.segs;
-        second.tree.segs$tipy <- second.tree.segs$basey + second.tree.segs$length2.c * cos(second.tree.segs$angle);
-        second.tree.segs$tipx <- second.tree.segs$basex + second.tree.segs$length2.c * sin(second.tree.segs$angle);
-
-        second.tree.segs.adjusted <- adply(
-            second.tree.segs,
-            .margins = 1,
-            .fun = function(r) {
-                offset.x  <- offset * cos(r$angle);
-                offset.y  <- offset * sin(r$angle);
-
-                if (r$angle > 0) {
-                    basey <- r$basey - offset.y;
-                    tipy <- r$tipy - offset.y;
-                } else {
-                    basey <- r$basey - offset.y;
-                    tipy <- r$tipy - offset.y;
-                    }
-
-                basex <- r$basex + offset.x;
-                tipx <- r$tipx + offset.x;
-
-                return(data.frame(basex, basey, tipx, tipy));
-                }
-            );
-
-        second.tree.segs.adjusted <- second.tree.segs.adjusted[which(!(second.tree.segs.adjusted$basey == second.tree.segs.adjusted$tipy & second.tree.segs.adjusted$basex == second.tree.segs.adjusted$tipx)),]
-        }
-
-    tree.out <- list(
-        tree.segs = tree.segs.adjusted,
-        tree.segs2 = second.tree.segs.adjusted
-        );
-
-    return(tree.out);
-    }
-
 get.seg.coords <- function(
     tree,
     v,
@@ -105,78 +9,62 @@ get.seg.coords <- function(
     # Calculate offset based on the line width
     offset <- offset / scale1 / 2;
 
-    tree.segs <- adply(
+    tree.segs <- apply(
         tree,
-        .margins = 1,
-        .fun = function(x) {
-            if (x$parent == -1) {
+        MARGIN = 1,
+        FUN = function(x) {
+            if (x['parent'] == -1) {
                 basey <- 0;
                 basex <- 0;
             } else {
-                basey <- v$y[v$id == x$parent];
-                basex <- v$x[v$id == x$parent];
+                basey <- v$y[v$id == x['parent']];
+                basex <- v$x[v$id == x['parent']];
                 }
 
-            tipy <- basey + x$length1 * cos(x$angle);
-            tipx <- basex + x$length1 * sin(x$angle);
+            tipy <- basey + x['length1'] * cos(x['angle']);
+            tipx <- basex + x['length1'] * sin(x['angle']);
 
-            return(data.frame(basex, basey, tipx, tipy));
+            data.frame(
+                basex = basex,
+                basey = basey,
+                tipx = tipx,
+                tipy = tipy
+                );
             }
         );
+    tree.segs <- as.data.frame(do.call('rbind', tree.segs));
+    rownames(tree.segs) <- rownames(tree);
+    tree.segs <- cbind(tree, tree.segs);
 
-    tree.out <- list();
     second.tree.segs.adjusted <- NULL;
 
-    tree.segs.adjusted <- adply(
-        tree.segs,
-        .margins = 1,
-        .fun = function(r) {
-            offset.x <- offset * cos(r$angle);
-            offset.y  <- offset * sin(r$angle);
-
-            if (r$angle > 0) {
-                basey <- r$basey + offset.y;
-                tipy <- r$tipy + offset.y;
-            } else {
-                basey <- r$basey + offset.y;
-                tipy <- r$tipy + offset.y;
-                }
-
-            basex <- r$basex - offset.x;
-            tipx <- r$tipx - offset.x;
+    tree.segs.adjusted <- tree.segs;
+    offset.x <- offset * cos(tree.segs.adjusted$angle);
+    offset.y <- offset * sin(tree.segs.adjusted$angle);
 
-            return(data.frame(basex, basey, tipx, tipy));
-            }
-        );
+    tree.segs.adjusted$basey <- tree.segs.adjusted$basey + offset.y;
+    tree.segs.adjusted$tipy <- tree.segs.adjusted$tipy + offset.y;
+    tree.segs.adjusted$basex <- tree.segs.adjusted$basex - offset.x;
+    tree.segs.adjusted$tipx <- tree.segs.adjusted$tipx - offset.x;
 
     if (length(grep('length',colnames(tree))) == 4) {
-        second.tree.segs <- tree.segs;
-        second.tree.segs$tipy <- second.tree.segs$basey + second.tree.segs$length2.c * cos(second.tree.segs$angle);
-        second.tree.segs$tipx <- second.tree.segs$basex + second.tree.segs$length2.c * sin(second.tree.segs$angle);
-
-
-        second.tree.segs.adjusted <- adply(
-            second.tree.segs,
-            .margins = 1,
-            .fun = function(r) {
-                offset.x  <- offset * cos(r$angle);
-                offset.y  <- offset * sin(r$angle);
-
-                if (r$angle > 0) {
-                    basey <- r$basey - offset.y;
-                    tipy <- r$tipy - offset.y;
-                } else {
-                    basey <- r$basey - offset.y;
-                    tipy <- r$tipy - offset.y;
-                    }
-
-                basex <- r$basex + offset.x;
-                tipx <- r$tipx + offset.x;
-
-                return(data.frame(basex, basey, tipx, tipy));
-                }
+        second.tree.segs.adjusted <- tree.segs;
+        second.tree.segs.adjusted$tipy <- (
+            second.tree.segs.adjusted$basey
+            + second.tree.segs.adjusted$length2.c
+            * cos(second.tree.segs.adjusted$angle)
+            );
+        second.tree.segs.adjusted$tipx <- (
+            second.tree.segs.adjusted$basex
+            + second.tree.segs.adjusted$length2.c
+            * sin(second.tree.segs.adjusted$angle)
             );
 
+        second.tree.segs.adjusted$basey <- second.tree.segs.adjusted$basey - offset.y;
+        second.tree.segs.adjusted$tipy <- second.tree.segs.adjusted$tipy - offset.y;
+        second.tree.segs.adjusted$basex <- second.tree.segs.adjusted$basex + offset.x;
+        second.tree.segs.adjusted$tipx <- second.tree.segs.adjusted$tipx + offset.x;
+
         second.tree.segs.adjusted <- second.tree.segs.adjusted[
             which(second.tree.segs.adjusted$basey != second.tree.segs.adjusted$tipy), ];
         }
diff --git a/R/add.text.R b/R/add.text.R
index 2832858..85c0225 100644
--- a/R/add.text.R
+++ b/R/add.text.R
@@ -61,18 +61,11 @@ check.overlap <- function(
 
     node.text.xrange <- c(left, right);
 
-    node.segs <- adply(
-        tree.max.adjusted[, c('tip', 'parent', 'x', 'y')],
-        .margins = 1,
-        .fun = function(w) {
-            data.frame(
-                y0 = (w$y + node.radius),
-                y1 = (w$y - node.radius),
-                x0 = (w$x - node.radius),
-                x1 = (w$x + node.radius)
-                );
-            }
-        );
+    node.segs <- tree.max.adjusted[, c('tip', 'parent', 'x', 'y')];
+    node.segs$y0 <- tree.max.adjusted$y + node.radius;
+    node.segs$y1 <- tree.max.adjusted$y - node.radius;
+    node.segs$x0 <- tree.max.adjusted$x - node.radius;
+    node.segs$x1 <- tree.max.adjusted$x + node.radius;
 
     line.intercept <- logical(length = nrow(tree.max.adjusted));
     node.intercept <- logical(length = nrow(tree.max.adjusted));
@@ -503,98 +496,56 @@ add.text2 <- function(
     # Radius in native units
     node.radius <- node.radius / scale;
     node.text <- node.text[node.text$node %in% tree$tip, ];
-    node.list <- alply(
-        seq_len(nrow(tree)),
-        .margins = 1,
-        .fun = function(x) {
-            return(character())
-            }
-        );
 
-    node.text.col <- node.list;
-    node.text.fontface <- node.list;
-
-    a_ply(
-        seq_len(
-            nrow(node.text)),
-        .margins = 1,
-        .fun = function(x) {
-            text.row <- node.text[x, ];
-            pos <- which(tree$tip == text.row$node);
-            text.value <- text.row$name;
-
-            if (length(grep('_', text.value)) > 0) {
-                text.split <- strsplit(text.value, split = '_')[[1]];
-                node.text.value <- text.split[1];
-                amp <- text.split[2];
-                call <- paste0(node.text.value, '^\'A', amp, '\'');
-                text.value <- parse(text = call);
-                }
+    node.list <- data.frame(row.names = rownames(tree));
+    node.text.col <- node.text.fontface <- lapply
 
-            node.list[[pos]] <<- c(node.list[[pos]], text.value);
-
-            node.text.col[[pos]] <<- c(
-                node.text.col[[pos]],
-                if (!is.na(text.row$col)) text.row$col else 'black'
-                );
-
-            node.text.fontface[[pos]] <<- c(
-                node.text.fontface[[pos]],
-                if (!is.na(text.row$fontface)) text.row$fontface else 'plain'
-                );
-            }
-        );
-
-    tree.max <- adply(
+    tree.max.adjusted <- apply(
         tree,
-        .margins = 1,
-        .fun = function(x) {
-            if (x$parent == -1) {
+        MARGIN = 1,
+        FUN = function(x) {
+            if (x['parent'] == -1) {
                 basex <- 0;
                 basey <- 0;
             } else {
-                basex <- v$x[v$id == x$parent];
-                basey <- v$y[v$id == x$parent];
+                basex <- v$x[v$id == x['parent']];
+                basey <- v$y[v$id == x['parent']];
                 }
 
-            tipx <- v$x[v$id == x$tip];
-            tipy <- v$y[v$id == x$tip];
+            tipx <- v$x[v$id == x['tip']];
+            tipy <- v$y[v$id == x['tip']];
 
             return(data.frame(basex, basey, tipx, tipy));
             }
         );
-
-    #the length of the visible line segments
-    tree.max.adjusted <- adply(
-        tree.max,
-        .margins = 1,
-        .fun = function(x) {
-            if (x$tipx == x$basex) {
-                #straight line
-                basex <- x$basex;
-                tipx <- x$tipx;
-                basey <- x$basey + node.radius;
-                tipy <- x$tipy - node.radius;
-            } else if (x$tipx > x$basex) {
-                basey <- x$basey + node.radius * cos(x$angle);
-                tipy <- x$tipy - node.radius * cos(x$angle);
-                basex <- x$basex + node.radius * sin(x$angle);
-                tipx <- x$tipx - node.radius * sin(x$angle);
-            } else if (x$tipx < x$basex) {
-                basey <- x$basey + node.radius * cos(x$angle);
-                tipy <- x$tipy - node.radius * cos(x$angle);
-                basex <- x$basex + node.radius * sin(x$angle);
-                tipx <- x$tipx - node.radius * sin(x$angle);
-                }
-            if (x$parent == -1) {
-                basex <- basey <- 0;
-                }
-
-            return(data.frame(basex,basey,tipx,tipy));
-            }
+    tree.max.adjusted <- do.call('rbind', tree.max.adjusted);
+    rownames(tree.max.adjusted) <- rownames(tree);
+    tree.max.adjusted <- cbind(tree, tree.max.adjusted);
+    tree.max <- tree.max.adjusted;
+
+    # 1 if positive angle, -1 if negative (or 0 degrees)
+    angle.modifier <- (tree.max.adjusted$angle > 0) * 2 - 1;
+
+    # Length of the visible line segments
+    tree.max.adjusted$basex <- (
+        tree.max.adjusted$basex +
+        angle.modifier * node.radius * sin(tree.max.adjusted$angle)
+        );
+    tree.max.adjusted$tipx <- (
+        tree.max.adjusted$tipx -
+        -angle.modifier * node.radius * sin(tree.max.adjusted$angle)
+        );
+    tree.max.adjusted$basey <- (
+        tree.max.adjusted$basey +
+        angle.modifier * node.radius * cos(tree.max.adjusted$angle)
+        );
+    tree.max.adjusted$tipy <- (
+        tree.max.adjusted$tipy -
+        -angle.modifier * node.radius * cos(tree.max.adjusted$angle)
         );
 
-    #push a viewport the same size as the final panel so we can do calculations based on absolute size units
+    # Push a viewport the same size as the final panel
+    # to perform calculations using absolute size units
     if (!is.null(clone.out)) {
         pushViewport(clone.out$vp);
     } else {
diff --git a/R/adjust.tree.R b/R/adjust.tree.R
index 220ab3e..4f29ffa 100644
--- a/R/adjust.tree.R
+++ b/R/adjust.tree.R
@@ -1,29 +1,26 @@
-adjust.lengths <- function(x, cols, node.df) {
-    out.df <- x;
-
-    for (column in cols) {
-        if (x[1, column] > 0) {
-            length.adj <- x[1, column];
+adjust.lengths <- function(x, length.cols, node.df) {
+    adjusted <- list();
+    for (column in length.cols) {
+        if (x[column] > 0) {
+            length.adj <- x[column];
 
             #  Max
-            if (x[1, column] == x[1, cols[length(cols)]]) {
-                length.adj <- length.adj + node.df$node.radius[node.df$id == x$tip];
+            if (x[column] == x[length.cols[length(length.cols)]]) {
+                length.adj <- length.adj + node.df$node.radius[node.df$id == x['tip']];
                 }
 
-            if (x$parent != -1) {
-                length.adj <- length.adj + node.df$node.radius[node.df$id == x$parent];
+            if (x['parent'] != -1) {
+                length.adj <- length.adj + node.df$node.radius[node.df$id == x['parent']];
                 }
-
         } else {
             length.adj <- 0;
             }
 
         var.name <- paste0(names(x)[column], '.adj');
-        out.df <- cbind(out.df, length.adj);
-        colnames(out.df)[ncol(out.df)] <- var.name;
+        adjusted[var.name] <- length.adj;
         }
 
-    return(out.df);
+    return(as.data.frame(adjusted));
     }
 
 adjust.branch.lengths <- function(node.df, tree, node.radius, scale1) {
@@ -35,13 +32,14 @@ adjust.branch.lengths <- function(node.df, tree, node.radius, scale1) {
     node.df$node.radius[node.df$id == -1] <- 0;
     length.cols <- grep('length', colnames(tree));
 
-    tree.adj <- adply(
+    tree.adj <- apply(
         tree,
-        .margins = 1,
-        .fun = function(x) {
-            adjust.lengths(x, length.cols, node.df);
-            }
+        MARGIN = 1,
+        FUN = function(x) adjust.lengths(x, length.cols, node.df)
         );
+    tree.adj <- do.call('rbind', tree.adj);
+    rownames(tree.adj) <- rownames(tree);
+    tree.adj <- cbind(tree, tree.adj);
 
     tree$length <- tree.adj$length.adj;
     tree$length1 <- tree.adj$length1.adj;
@@ -49,26 +47,3 @@ adjust.branch.lengths <- function(node.df, tree, node.radius, scale1) {
 
     return(tree);
     }
-
-adjust.tree <- function(in.tree.node.radius, tree.in, node.radius, scale.x.real) {
-    if (is.null(in.tree.node.radius$node.radius)) {
-        node.radius <- node.radius / scale.x.real;
-        in.tree.node.radius$node.radius <- rep(node.radius, nrow(in.tree.node.radius));
-        }
-
-    in.tree.node.radius$node.radius[in.tree.node.radius$id == -1] <- 0;
-    length.cols <- grep('length', colnames(tree.in));
-    tree.adj <- adply(
-        tree.in,
-        .margins = 1,
-        .fun = function(x) {
-            adjust.lengths(x, length.cols, in.tree.node.radius);
-            }
-        );
-
-    tree.in$length <- tree.adj$length.adj;
-    tree.in$length1 <- tree.adj$length1.adj;
-    tree.in$length2.c <- tree.adj$length2.c.adj;
-
-    return(tree.in);
-    }
diff --git a/tests/testthat/helper-compare.R b/tests/testthat/helper-compare.R
index b929b71..0d175d4 100644
--- a/tests/testthat/helper-compare.R
+++ b/tests/testthat/helper-compare.R
@@ -13,7 +13,7 @@ compare.trees <- function(example, test) {
         }
 
     get.axis.keys <- function(x) {
-        stringr::str_subset(x$childrenOrder, 'axis');
+        x$childrenOrder[grepl('axis', x$childrenOrder)];
         }
 
     # Grob comparisons
@@ -172,7 +172,7 @@ compare.trees <- function(example, test) {
 
     test.polygon.grobs <- function(example, test) {
         get.polygon.keys <- function(x) {
-            stringr::str_subset(x$childrenOrder, 'polygon')
+            x$childrenOrder[grepl('polygon', x$childrenOrder)];
             }
 
         compare.polygons <- function(x, y) {