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Improve Seurat and ggplot compatibility #95

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merged 7 commits into from
Nov 5, 2023
Merged

Improve Seurat and ggplot compatibility #95

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cb0256d
Merge branch 'master' into develop
lazappi Jun 27, 2022
35a4bb0
Minor updates for compatibility with Seurat v5
lazappi Oct 24, 2023
dfab864
Minor changes to avoid warnings from ggplot2/tidyselect
lazappi Oct 24, 2023
3f3b92f
Add missing NEWS changes
lazappi Oct 24, 2023
155736a
Merge remote-tracking branch 'origin/main' into develop
lazappi Nov 5, 2023
fffdfde
Restrict vignette section to Seurat >= 5.0.0
lazappi Nov 5, 2023
a6981fd
Mark internal functions
lazappi Nov 5, 2023
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8 changes: 4 additions & 4 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
Package: clustree
Type: Package
Title: Visualise Clusterings at Different Resolutions
Version: 0.5.0
Date: 2022-06-24
Version: 0.5.0.9001
Date: 2023-10-24
Authors@R:
c(person("Luke", "Zappia", role = c("aut", "cre"),
email = "[email protected]",
Expand Down Expand Up @@ -33,7 +33,7 @@ Imports: checkmate,
igraph,
dplyr,
grid,
ggplot2,
ggplot2 (>= 3.4.0),
viridis,
methods,
rlang,
Expand All @@ -50,5 +50,5 @@ Suggests:
pkgdown,
spelling
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.0
RoxygenNote: 7.2.3
Language: en-GB
12 changes: 12 additions & 0 deletions NEWS.md
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@@ -1,3 +1,15 @@
# clustree (development version)

### _clustree_ 0.5.0.9001 (2023-10-24)

* Avoid warnings due to deprecated functionality in _ggplot2_ and
_tidyselect_. Includes increasing the _ggplot2_ requirement to >= 3.4.0.
(Fixes #35)

### _clustree_ 0.5.0.9000 (2023-10-24)

* Minor updates for compatibility with upcoming _Seurat_ v5 release (Fixes #93)

# _clustree_ 0.5.0 (2022-06-24)

## Minor changes
Expand Down
8 changes: 8 additions & 0 deletions R/checks.R
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Expand Up @@ -9,6 +9,8 @@
#' @param node_aes value of the node aesthetic to check
#' @param node_aes_aggr aggregation function associated with the node aesthetic
#'
#' @keywords internal
#'
#' @importFrom utils head
assert_node_aes <- function(node_aes_name, prefix, metadata, node_aes,
node_aes_aggr) {
Expand Down Expand Up @@ -58,6 +60,8 @@ assert_node_aes <- function(node_aes_name, prefix, metadata, node_aes,
#' @param node_aes_aggr aggregation function associated with the node aesthetic
#' @param min minimum numeric value allowed
#' @param max maximum numeric value allowed
#'
#' @keywords internal
assert_numeric_node_aes <- function(node_aes_name, prefix, metadata, node_aes,
node_aes_aggr, min, max) {

Expand Down Expand Up @@ -87,6 +91,8 @@ assert_numeric_node_aes <- function(node_aes_name, prefix, metadata, node_aes,
#' @param min minimum numeric value allowed
#' @param max maximum numeric value allowed
#'
#' @keywords internal
#'
#' @importFrom grDevices col2rgb
assert_colour_node_aes <- function(node_aes_name, prefix, metadata, node_aes,
node_aes_aggr, min, max) {
Expand Down Expand Up @@ -120,6 +126,8 @@ assert_colour_node_aes <- function(node_aes_name, prefix, metadata, node_aes,
#'
#' @param node_aes_list List of node aesthetics
#'
#' @keywords internal
#'
#' @return Corrected node aesthetics list
check_node_aes_list <- function(node_aes_list) {
for (aes in names(node_aes_list)) {
Expand Down
62 changes: 36 additions & 26 deletions R/clustree.R
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Expand Up @@ -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) {
Expand All @@ -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))) {
Expand Down Expand Up @@ -516,8 +517,13 @@ clustree.Seurat <- function(x, prefix = paste0(assay, "_snn_res."),
)
}
aes_name <- paste0(exprs, "_", node_aes_name)
x[[aes_name]] <- Seurat::FetchData(x, vars = node_aes_value,
slot = exprs)
if (packageVersion("SeuratObject") >= package_version("5.0.0")) {
x[[aes_name]] <- Seurat::FetchData(x, vars = node_aes_value,
layer = exprs)
} else {
x[[aes_name]] <- Seurat::FetchData(x, vars = node_aes_value,
slot = exprs)
}
args[[node_aes]] <- aes_name
}
}
Expand All @@ -541,6 +547,8 @@ clustree.Seurat <- function(x, prefix = paste0(assay, "_snn_res."),
#' name of a metadata column to use for node transparency
#' @param allowed vector of allowed node attributes to use as aesthetics
#'
#' @keywords internal
#'
#' @importFrom ggraph geom_node_point
#' @importFrom ggplot2 aes_
add_node_points <- function(node_colour, node_size, node_alpha, allowed) {
Expand All @@ -555,25 +563,25 @@ 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,
Expand All @@ -597,6 +605,8 @@ add_node_points <- function(node_colour, node_size, node_alpha, allowed) {
#' labels
#' @param allowed vector of allowed node attributes to use as aesthetics
#'
#' @keywords internal
#'
#' @importFrom ggraph geom_node_label
#' @importFrom ggplot2 aes_
add_node_labels <- function(node_label, node_colour, node_label_size,
Expand All @@ -605,13 +615,13 @@ 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,
Expand Down
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