Minor changes to avoid warnings from ggplot2/tidyselect

Increase ggplot2 requirement to >= 3.4.0

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: clustree
 Type: Package
 Title: Visualise Clusterings at Different Resolutions
-Version: 0.5.0.9000
+Version: 0.5.0.9001
 Date: 2023-10-24
 Authors@R:
  c(person("Luke", "Zappia", role = c("aut", "cre"),
@@ -33,7 +33,7 @@ Imports: checkmate,
  igraph,
  dplyr,
  grid,
- ggplot2,
+ ggplot2 (>= 3.4.0),
  viridis,
  methods,
  rlang,

NEWS.md

@@ -1,5 +1,10 @@
 # clustree (development version)
 
+### _clustree_ 0.5.0.9001 (2023-10-24)
+
+* Avoid warnings due to deprecated functionality in _ggplot2_ and
+ _tidyselect_ (Fixes #35)
+
 ### _clustree_ 0.5.0.9000 (2023-10-24)
 
 * Minor updates for compatibility with upcoming _Seurat_ v5 release (Fixes #93)

R/clustree.R

@@ -284,13 +284,14 @@ clustree.matrix <- function(x, prefix,
  ends = edge_arrow_ends),
  end_cap = circle(circle_size_end, "points"),
  start_cap = circle(circle_size_start, "points"),
- aes_(colour = ~count,
-  alpha = ~in_prop,
-  edge_width = ~is_core))
+ aes(colour = .data$count,
+ alpha = .data$in_prop,
+ edge_width = .data$is_core))
 
  } else {
- gg <- gg + geom_edge_link(aes_(colour = ~count, alpha = ~in_prop,
- edge_width = ~is_core))
+ gg <- gg + geom_edge_link(aes(colour = .data$count,
+ alpha = .data$in_prop,
+ edge_width = .data$is_core))
  }
 
  if (highlight_core) {
@@ -311,17 +312,17 @@ clustree.matrix <- function(x, prefix,
 
  # Plot node text
  if (scale_node_text && !is.numeric(node_size)) {
- gg <- gg + geom_node_text(aes_(label = ~cluster,
-  size = as.name(graph_attr$node_size)),
+ gg <- gg + geom_node_text(aes(label = .data$cluster,
+ size = .data[[graph_attr$node_size]]),
  colour = node_text_colour,
  angle = node_text_angle
  )
  } else {
- gg <- gg + geom_node_text(aes_(label = ~cluster),
+ gg <- gg + geom_node_text(aes(label = .data$cluster),
  size = node_text_size,
  colour = node_text_colour,
  angle = node_text_angle
-  )
+ )
  }
 
  if (!(is.null(node_label))) {
@@ -560,25 +561,25 @@ add_node_points <- function(node_colour, node_size, node_alpha, allowed) {
  }
 
  switch(aes_allowed,
- col_size_alpha = geom_node_point(aes_(colour = as.name(node_colour),
-  size = as.name(node_size),
-  alpha = as.name(node_alpha))),
- col_alpha = geom_node_point(aes_(colour = as.name(node_colour),
-  alpha = as.name(node_alpha)),
+ col_size_alpha = geom_node_point(aes(colour = .data[[node_colour]],
+ size = .data[[node_size]],
+ alpha = .data[[node_alpha]])),
+ col_alpha = geom_node_point(aes(colour = .data[[node_colour]],
+ alpha = .data[[node_alpha]]),
  size = node_size),
- col_size = geom_node_point(aes_(colour = as.name(node_colour),
-  size = as.name(node_size)),
+ col_size = geom_node_point(aes(colour = .data[[node_colour]],
+ size = .data[[node_size]]),
  alpha = node_alpha),
- col = geom_node_point(aes_(colour = as.name(node_colour)),
+ col = geom_node_point(aes(colour = .data[[node_colour]]),
  size = node_size,
  alpha = node_alpha),
- size_alpha = geom_node_point(aes_(size = as.name(node_size),
-  alpha = as.name(node_alpha)),
+ size_alpha = geom_node_point(aes(size = .data[[node_size]],
+ alpha = .data[[node_alpha]]),
  colour = node_colour),
- size = geom_node_point(aes_(size = as.name(node_size)),
+ size = geom_node_point(aes(size = .data[[node_size]]),
  colour = node_colour,
  alpha = node_alpha),
- alpha = geom_node_point(aes_(alpha = as.name(node_alpha)),
+ alpha = geom_node_point(aes(alpha = .data[[node_alpha]]),
  colour = node_colour,
  size = node_size),
  none = geom_node_point(colour = node_colour,
@@ -610,13 +611,13 @@ add_node_labels <- function(node_label, node_colour, node_label_size,
  is_allowed <- c(node_colour) %in% allowed
 
  if (is_allowed) {
- geom_node_label(aes_(label = as.name(node_label),
-  fill = as.name(node_colour)),
+ geom_node_label(aes(label = .data[[node_label]],
+ fill = .data[[node_colour]]),
  size = node_label_size,
  colour = node_label_colour,
  nudge_y = node_label_nudge)
  } else {
- geom_node_label(aes_(label = as.name(node_label)),
+ geom_node_label(aes(label = .data[[node_label]]),
  fill = node_colour,
  size = node_label_size,
  colour = node_label_colour,

R/clustree_overlay.R

@@ -259,12 +259,12 @@ clustree_overlay.matrix <- function(x, prefix, metadata, x_value, y_value,
  levels(edges[[paste0("from_", prefix)]]) <- levels(nodes[[prefix]])
 
  if (use_colour == "points") {
- gg <- ggplot(points, aes_(x = as.name(x_value), y = as.name(y_value))) +
- geom_point(aes_(colour = as.name(paste0(hi_res, "_cluster"))),
+ gg <- ggplot(points, aes(x = .data[[x_value]], y = .data[[y_value]])) +
+ geom_point(aes(colour = .data[[paste0(hi_res, "_cluster")]]),
  size = point_size, alpha = point_alpha,
  shape = point_shape)
  } else {
- gg <- ggplot(points, aes_(x = as.name(x_value), y = as.name(y_value))) +
+ gg <- ggplot(points, aes(x = .data[[x_value]], y = .data[[y_value]])) +
  geom_point(colour = alt_colour, size = point_size,
  alpha = point_alpha, shape = point_shape)
  }
@@ -283,36 +283,36 @@ clustree_overlay.matrix <- function(x, prefix, metadata, x_value, y_value,
  if (use_colour == "edges") {
  gg <- gg +
  geom_segment(data = edges_res,
- aes_(x = as.name(paste0("from_", x_value)),
-  y = as.name(paste0("from_", y_value)),
-  xend = as.name(paste0("to_", x_value)),
-  yend = as.name(paste0("to_", y_value)),
-  alpha = ~ in_prop,
-  colour = as.name(paste0("from_", prefix))),
+ aes(x = .data[[paste0("from_", x_value)]],
+ y = .data[[paste0("from_", y_value)]],
+ xend = .data[[paste0("to_", x_value)]],
+ yend = .data[[paste0("to_", y_value)]],
+ alpha = .data$in_prop,
+ colour = .data[[paste0("from_", prefix)]]),
  arrow = arrow(length = unit(edge_width * 5,
  "points")),
- size = edge_width)
+ linewidth = edge_width)
  } else {
  gg <- gg +
  geom_segment(data = edges_res,
- aes_(x = as.name(paste0("from_", x_value)),
-  y = as.name(paste0("from_", y_value)),
-  xend = as.name(paste0("to_", x_value)),
-  yend = as.name(paste0("to_", y_value)),
-  alpha = ~ in_prop),
+ aes(x = .data[[paste0("from_", x_value)]],
+ y = .data[[paste0("from_", y_value)]],
+ xend = .data[[paste0("to_", x_value)]],
+ yend = .data[[paste0("to_", y_value)]],
+ alpha = .data$in_prop),
  arrow = arrow(length = unit(edge_width * 5,
  "points")),
- size = edge_width,
+ linewidth = edge_width,
  colour = alt_colour)
  }
  }
 
  if (label_nodes) {
  gg <- gg +
  ggrepel::geom_label_repel(data = nodes,
- aes_(x = as.name(x_val),
-  y = as.name(y_val),
-  label = ~ node),
+ aes(x = .data[[x_val]],
+ y = .data[[y_val]],
+ label = .data$node),
  size = label_size)
  }
 
@@ -658,57 +658,57 @@ overlay_node_points <- function(nodes, x_value, y_value, node_colour, node_size,
 
  switch(aes_allowed,
  col_size_alpha = geom_point(data = nodes,
- aes_(x = as.name(x_value),
-  y = as.name(y_value),
-  fill = as.name(node_colour),
-  size = as.name(node_size),
-  alpha = as.name(node_alpha)),
+ aes(x = .data[[x_value]],
+ y = .data[[y_value]],
+ fill = .data[[node_colour]],
+ size = .data[[node_size]],
+ alpha = .data[[node_alpha]]),
  shape = 21),
  col_alpha = geom_point(data = nodes,
- aes_(x = as.name(x_value),
-  y = as.name(y_value),
-  fill = as.name(node_colour),
-  alpha = as.name(node_alpha)),
+ aes(x = .data[[x_value]],
+ y = .data[[y_value]],
+ fill = .data[[node_colour]],
+ alpha = .data[[node_alpha]]),
  size = node_size,
  shape = 21),
  col_size = geom_point(data = nodes,
- aes_(x = as.name(x_value),
-  y = as.name(y_value),
-  fill = as.name(node_colour),
-  size = as.name(node_size)),
+ aes(x = .data[[x_value]],
+ y = .data[[y_value]],
+ fill = .data[[node_colour]],
+ size = .data[[node_size]]),
  alpha = node_alpha,
  shape = 21),
  col = geom_point(data = nodes,
- aes_(x = as.name(x_value),
-  y = as.name(y_value),
-  fill = as.name(node_colour)),
+ aes(x = .data[[x_value]],
+ y = .data[[y_value]],
+ fill = .data[[node_colour]]),
  size = node_size,
  alpha = node_alpha,
  shape = 21),
  size_alpha = geom_point(data = nodes,
- aes_(x = as.name(x_value),
-  y = as.name(y_value),
-  fill = as.name(node_size),
-  alpha = as.name(node_alpha)),
+ aes(x = .data[[x_value]],
+ y = .data[[y_value]],
+ fill = .data[[node_size]],
+ alpha = .data[[node_alpha]]),
  colour = node_colour,
  shape = 21),
  size = geom_point(data = nodes,
- aes_(x = as.name(x_value),
-  y = as.name(y_value),
-  size = as.name(node_size)),
+ aes(x = .data[[x_value]],
+ y = .data[[y_value]],
+ size = .data[[node_size]]),
  fill = node_colour,
  alpha = node_alpha,
  shape = 21),
  alpha = geom_point(data = nodes,
- aes_(x = as.name(x_value),
-  y = as.name(y_value),
-  alpha = as.name(node_alpha)),
+ aes(x = .data[[x_value]],
+ y = .data[[y_value]],
+ alpha = .data[[node_alpha]]),
  fill = node_colour,
  size = node_size,
  shape = 21),
  none = geom_point(data = nodes,
- aes_(x = as.name(x_value),
-  y = as.name(y_value)),
+ aes(x = .data[[x_value]],
+ y = .data[[y_value]]),
  fill = node_colour,
  size = node_size,
  alpha = node_alpha,
@@ -776,14 +776,13 @@ plot_overlay_side <- function(nodes, edges, points, prefix, side_value,
  !!as.name(paste0("to_", prefix)))))
 
  if (use_colour == "points") {
-
- gg <- ggplot(points, aes_(x = as.name(side_value), y = point_y)) +
- geom_jitter(aes_(colour = as.name(colnames(points)[3])),
+ gg <- ggplot(points, aes(x = .data[[side_value]], y = point_y)) +
+ geom_jitter(aes(colour = .data[[colnames(points)[3]]]),
  height = y_jitter * median(y_diffs), width = 0,
  size = point_size, alpha = point_alpha,
  shape = point_shape)
  } else {
- gg <- ggplot(points, aes_(x = as.name(side_value), y = point_y)) +
+ gg <- ggplot(points, aes(x = .data[[side_value]], y = point_y)) +
  geom_jitter(height = y_jitter * median(y_diffs), width = 0,
  colour = alt_colour, size = point_size,
  alpha = point_alpha, shape = point_shape)
@@ -802,37 +801,37 @@ plot_overlay_side <- function(nodes, edges, points, prefix, side_value,
  if (use_colour == "edges") {
  gg <- gg +
  geom_segment(data = edges_res,
- aes_(x = as.name(paste0("from_", side_value)),
-  y = ~ from_y,
-  xend = as.name(paste0("to_", side_value)),
-  yend = ~ to_y,
-  alpha = ~ in_prop,
-  colour = as.name(paste0("from_", prefix))),
+ aes(x = .data[[paste0("from_", side_value)]],
+ y = .data$from_y,
+ xend = .data[[paste0("to_", side_value)]],
+ yend = .data$to_y,
+ alpha = .data$in_prop,
+ colour = .data[[paste0("from_", prefix)]]),
  arrow = arrow(length = unit(edge_width * 5,
  "points")),
- size = edge_width)
+ linewidth = edge_width)
  } else {
  gg <- gg +
  geom_segment(data = edges_res,
- aes_(x = as.name(paste0("from_", side_value)),
-  y = ~ from_y,
-  xend = as.name(paste0("to_", side_value)),
-  yend = ~ to_y,
-  alpha = ~ in_prop),
+ aes(x = .data[[paste0("from_", side_value)]],
+ y = .data$from_y,
+ xend = .data[[paste0("to_", side_value)]],
+ yend = .data$to_y,
+ alpha = .data$in_prop),
  arrow = arrow(length = unit(edge_width * 5,
  "points")),
- size = edge_width,
+ linewidth = edge_width,
  colour = alt_colour)
  }
  }
 
  if (label_nodes) {
  gg <- gg +
  ggrepel::geom_label_repel(data = nodes,
- aes_(x = as.name(paste0("mean_",
-  side_value)),
-  y = ~ y,
-  label = ~ node),
+ aes(x = .data[[paste0("mean_",
+ side_value)]],
+ y = .data$y,
+ label = .data$node),
  size = label_size)
  }
 
@@ -843,8 +842,8 @@ plot_overlay_side <- function(nodes, edges, points, prefix, side_value,
  scale_colour_hue(drop = FALSE) +
  ylab(prefix) +
  theme_minimal() +
- theme(axis.line.x = element_line(size = 1, colour = "grey50"),
- axis.ticks.x = element_line(size = 0.6, colour = "grey50"),
+ theme(axis.line.x = element_line(linewidth = 1, colour = "grey50"),
+ axis.ticks.x = element_line(linewidth = 0.6, colour = "grey50"),
  panel.grid.major.x = element_blank(),
  panel.grid.minor.x = element_blank(),
  panel.grid.minor.y = element_blank())