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Improves DimHeatmap documentation and default behavior when fast=FALSE (Issue #9810) #9813

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Improves DimHeatmap documentation and default behavior when fast=FALSE (Issue #9810) #9813

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43 changes: 25 additions & 18 deletions R/visualization.R
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@anashen anashen Sep 25, 2025

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The function documentation will need to be updated to also import plot_layout (line 47):

#' @importFrom patchwork wrap_plots plot_layout

Otherwise, users will receive an error running DimHeatmap when the patchwork package isn't loaded (Error in plot_layout(guides = "collect") : could not find function "plot_layout").

Original file line number Diff line number Diff line change
Expand Up @@ -34,10 +34,11 @@ setGeneric(
#' @param balanced Plot an equal number of genes with both + and - scores.
#' @param projected Use the full projected dimensional reduction
#' @param ncol Number of columns to plot
#' @param fast If true, use \code{image} to generate plots; faster than using ggplot2, but not customizable
#' @param fast If true, use \code{image} to generate plots; faster than using ggplot2, but not customizable and excludes figure legend in output
#' @param assays A vector of assays to pull data from
#' @param combine Combine plots into a single \code{\link[patchwork]{patchwork}ed}
#' @param combine Combine plots into a single \code{\link[patchwork]{patchwork}ed} with single shared figure legend when \code{fast=FALSE}
#' ggplot object. If \code{FALSE}, return a list of ggplot objects
Comment on lines +39 to 40
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Suggested change
#' @param combine Combine plots into a single \code{\link[patchwork]{patchwork}ed} with single shared figure legend when \code{fast=FALSE}
#' ggplot object. If \code{FALSE}, return a list of ggplot objects
#' @param combine Combine plots into a single \code{\link[patchwork]{patchwork}ed} ggplot object with
#' single shared figure legend when \code{fast=FALSE}. If \code{FALSE}, return a list of ggplot objects

#' @param leg.pos When \code{combine=TRUE}, allows legend position to be adjusted for \code{\link[patchwork]{patchwork}ed} output; defaults as \code{"right"}
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Suggested change
#' @param leg.pos When \code{combine=TRUE}, allows legend position to be adjusted for \code{\link[patchwork]{patchwork}ed} output; defaults as \code{"right"}
#' @param legend.position When \code{combine=TRUE}, allows legend position to be adjusted for \code{\link[patchwork]{patchwork}ed} output; defaults as \code{"right"}

Renaming this parameter to legend.position would make its purpose a bit more clear to users.

#'
#' @return No return value by default. If using fast = FALSE, will return a
#' \code{\link[patchwork]{patchwork}ed} ggplot object if combine = TRUE, otherwise
Expand All @@ -54,21 +55,22 @@ setGeneric(
#' DimHeatmap(object = pbmc_small)
#'
DimHeatmap <- function(
object,
dims = 1,
nfeatures = 30,
cells = NULL,
reduction = 'pca',
disp.min = -2.5,
disp.max = NULL,
balanced = TRUE,
projected = FALSE,
ncol = NULL,
fast = TRUE,
raster = TRUE,
slot = 'scale.data',
assays = NULL,
combine = TRUE
object,
dims = 1,
nfeatures = 30,
cells = NULL,
reduction = 'pca',
disp.min = -2.5,
disp.max = NULL,
balanced = TRUE,
projected = FALSE,
ncol = NULL,
fast = TRUE,
raster = TRUE,
slot = 'scale.data',
assays = NULL,
combine = TRUE,
leg.pos = "right"
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Suggested change
leg.pos = "right"
legend.position = "right"

) {
ncol <- ncol %||% ifelse(test = length(x = dims) > 2, yes = 3, no = length(x = dims))
plots <- vector(mode = 'list', length = length(x = dims))
Expand Down Expand Up @@ -171,14 +173,19 @@ DimHeatmap <- function(
cell.order = dim.cells,
feature.order = dim.features
)
plots[[i]] <- plots[[i]] +
ggtitle(paste0(Key(object = object[[reduction]]), dims[i])) +
theme(plot.title = element_text(hjust = 0.5, face = "bold"))
}
}
if (fast) {
par(mfrow = orig.par)
return(invisible(x = NULL))
}
if (combine) {
plots <- wrap_plots(plots, ncol = ncol, guides = "collect")
plots <- wrap_plots(plots, ncol = ncol, guides = "collect") +
plot_layout(guides = "collect") &
theme(legend.position = leg.pos)
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Suggested change
theme(legend.position = leg.pos)
theme(legend.position = legend.position)

}
return(plots)
}
Expand Down