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visualization.R
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visualization.R
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#' @importFrom utils globalVariables
#' @importFrom ggplot2 fortify GeomViolin ggproto
#' @importFrom SeuratObject DefaultDimReduc
#'
NULL
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Generics
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#' @importFrom methods setGeneric
#'
setGeneric(
name = '.PrepImageData',
def = function(data, cells, ...) {
standardGeneric(f = '.PrepImageData')
}
)
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Heatmaps
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#' Dimensional reduction heatmap
#'
#' Draws a heatmap focusing on a principal component. Both cells and genes are sorted by their
#' principal component scores. Allows for nice visualization of sources of heterogeneity in the dataset.
#'
#' @inheritParams DoHeatmap
#' @param dims Dimensions to plot
#' @param nfeatures Number of genes to plot
#' @param cells A list of cells to plot. If numeric, just plots the top cells.
#' @param reduction Which dimensional reduction to use
#' @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 assays A vector of assays to pull data from
#' @param combine Combine plots into a single \code{\link[patchwork]{patchwork}ed}
#' ggplot object. If \code{FALSE}, return a list of ggplot objects
#'
#' @return No return value by default. If using fast = FALSE, will return a
#' \code{\link[patchwork]{patchwork}ed} ggplot object if combine = TRUE, otherwise
#' returns a list of ggplot objects
#'
#' @importFrom patchwork wrap_plots
#' @export
#' @concept visualization
#'
#' @seealso \code{\link[graphics]{image}} \code{\link[ggplot2]{geom_raster}}
#'
#' @examples
#' data("pbmc_small")
#' 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
) {
ncol <- ncol %||% ifelse(test = length(x = dims) > 2, yes = 3, no = length(x = dims))
plots <- vector(mode = 'list', length = length(x = dims))
assays <- assays %||% DefaultAssay(object = object)
disp.max <- disp.max %||% ifelse(
test = slot == 'scale.data',
yes = 2.5,
no = 6
)
if (!DefaultAssay(object = object[[reduction]]) %in% assays) {
warning("The original assay that the reduction was computed on is different than the assay specified")
}
cells <- cells %||% ncol(x = object)
if (is.numeric(x = cells)) {
cells <- lapply(
X = dims,
FUN = function(x) {
cells <- TopCells(
object = object[[reduction]],
dim = x,
ncells = cells,
balanced = balanced
)
if (balanced) {
cells$negative <- rev(x = cells$negative)
}
cells <- unlist(x = unname(obj = cells))
return(cells)
}
)
}
if (!is.list(x = cells)) {
cells <- lapply(X = 1:length(x = dims), FUN = function(x) {return(cells)})
}
features <- lapply(
X = dims,
FUN = TopFeatures,
object = object[[reduction]],
nfeatures = nfeatures,
balanced = balanced,
projected = projected
)
features.all <- unique(x = unlist(x = features))
if (length(x = assays) > 1) {
features.keyed <- lapply(
X = assays,
FUN = function(assay) {
features <- features.all[features.all %in% rownames(x = object[[assay]])]
if (length(x = features) > 0) {
return(paste0(Key(object = object[[assay]]), features))
}
}
)
features.keyed <- Filter(f = Negate(f = is.null), x = features.keyed)
features.keyed <- unlist(x = features.keyed)
} else {
features.keyed <- features.all
DefaultAssay(object = object) <- assays
}
data.all <- FetchData(
object = object,
vars = features.keyed,
cells = unique(x = unlist(x = cells)),
slot = slot
)
data.all <- MinMax(data = data.all, min = disp.min, max = disp.max)
data.limits <- c(min(data.all), max(data.all))
# if (check.plot && any(c(length(x = features.keyed), length(x = cells[[1]])) > 700)) {
# choice <- menu(c("Continue with plotting", "Quit"), title = "Plot(s) requested will likely take a while to plot.")
# if (choice != 1) {
# return(invisible(x = NULL))
# }
# }
if (fast) {
nrow <- floor(x = length(x = dims) / 3.01) + 1
orig.par <- par()$mfrow
par(mfrow = c(nrow, ncol))
}
for (i in 1:length(x = dims)) {
dim.features <- c(features[[i]][[2]], rev(x = features[[i]][[1]]))
dim.features <- rev(x = unlist(x = lapply(
X = dim.features,
FUN = function(feat) {
return(grep(pattern = paste0(feat, '$'), x = features.keyed, value = TRUE))
}
)))
dim.cells <- cells[[i]]
data.plot <- data.all[dim.cells, dim.features]
if (fast) {
SingleImageMap(
data = data.plot,
title = paste0(Key(object = object[[reduction]]), dims[i]),
order = dim.cells
)
} else {
plots[[i]] <- SingleRasterMap(
data = data.plot,
raster = raster,
limits = data.limits,
cell.order = dim.cells,
feature.order = dim.features
)
}
}
if (fast) {
par(mfrow = orig.par)
return(invisible(x = NULL))
}
if (combine) {
plots <- wrap_plots(plots, ncol = ncol, guides = "collect")
}
return(plots)
}
#' Feature expression heatmap
#'
#' Draws a heatmap of single cell feature expression.
#'
#' @param object Seurat object
#' @param features A vector of features to plot, defaults to \code{VariableFeatures(object = object)}
#' @param cells A vector of cells to plot
#' @param disp.min Minimum display value (all values below are clipped)
#' @param disp.max Maximum display value (all values above are clipped); defaults to 2.5
#' if \code{slot} is 'scale.data', 6 otherwise
#' @param group.by A vector of variables to group cells by; pass 'ident' to group by cell identity classes
#' @param group.bar Add a color bar showing group status for cells
#' @param group.colors Colors to use for the color bar
#' @param slot Data slot to use, choose from 'raw.data', 'data', or 'scale.data'
#' @param assay Assay to pull from
# @param check.plot Check that plotting will finish in a reasonable amount of time
#' @param label Label the cell identies above the color bar
#' @param size Size of text above color bar
#' @param hjust Horizontal justification of text above color bar
#' @param vjust Vertical justification of text above color bar
#' @param angle Angle of text above color bar
#' @param raster If true, plot with geom_raster, else use geom_tile. geom_raster may look blurry on
#' some viewing applications such as Preview due to how the raster is interpolated. Set this to FALSE
#' if you are encountering that issue (note that plots may take longer to produce/render).
#' @param draw.lines Include white lines to separate the groups
#' @param lines.width Integer number to adjust the width of the separating white lines.
#' Corresponds to the number of "cells" between each group.
#' @param group.bar.height Scale the height of the color bar
#' @param combine Combine plots into a single \code{\link[patchwork]{patchwork}ed}
#' ggplot object. If \code{FALSE}, return a list of ggplot objects
#'
#' @return A \code{\link[patchwork]{patchwork}ed} ggplot object if
#' \code{combine = TRUE}; otherwise, a list of ggplot objects
#'
#' @importFrom stats median
#' @importFrom scales hue_pal
#' @importFrom ggplot2 annotation_raster coord_cartesian scale_color_manual
#' ggplot_build aes_string geom_text
#' @importFrom patchwork wrap_plots
#' @export
#' @concept visualization
#'
#' @examples
#' data("pbmc_small")
#' DoHeatmap(object = pbmc_small)
#'
DoHeatmap <- function(
object,
features = NULL,
cells = NULL,
group.by = 'ident',
group.bar = TRUE,
group.colors = NULL,
disp.min = -2.5,
disp.max = NULL,
slot = 'scale.data',
assay = NULL,
label = TRUE,
size = 5.5,
hjust = 0,
vjust = 0,
angle = 45,
raster = TRUE,
draw.lines = TRUE,
lines.width = NULL,
group.bar.height = 0.02,
combine = TRUE
) {
cells <- cells %||% colnames(x = object)
if (is.numeric(x = cells)) {
cells <- colnames(x = object)[cells]
}
assay <- assay %||% DefaultAssay(object = object)
DefaultAssay(object = object) <- assay
features <- features %||% VariableFeatures(object = object)
features <- rev(x = unique(x = features))
disp.max <- disp.max %||% ifelse(
test = slot == 'scale.data',
yes = 2.5,
no = 6
)
# make sure features are present
possible.features <- rownames(x = GetAssayData(object = object, slot = slot))
if (any(!features %in% possible.features)) {
bad.features <- features[!features %in% possible.features]
features <- features[features %in% possible.features]
if(length(x = features) == 0) {
stop("No requested features found in the ", slot, " slot for the ", assay, " assay.")
}
warning("The following features were omitted as they were not found in the ", slot,
" slot for the ", assay, " assay: ", paste(bad.features, collapse = ", "))
}
data <- as.data.frame(x = as.matrix(x = t(x = GetAssayData(
object = object,
slot = slot)[features, cells, drop = FALSE])))
object <- suppressMessages(expr = StashIdent(object = object, save.name = 'ident'))
group.by <- group.by %||% 'ident'
groups.use <- object[[group.by]][cells, , drop = FALSE]
# group.use <- switch(
# EXPR = group.by,
# 'ident' = Idents(object = object),
# object[[group.by, drop = TRUE]]
# )
# group.use <- factor(x = group.use[cells])
plots <- vector(mode = 'list', length = ncol(x = groups.use))
for (i in 1:ncol(x = groups.use)) {
data.group <- data
group.use <- groups.use[, i, drop = TRUE]
if (!is.factor(x = group.use)) {
group.use <- factor(x = group.use)
}
names(x = group.use) <- cells
if (draw.lines) {
# create fake cells to serve as the white lines, fill with NAs
lines.width <- lines.width %||% ceiling(x = nrow(x = data.group) * 0.0025)
placeholder.cells <- sapply(
X = 1:(length(x = levels(x = group.use)) * lines.width),
FUN = function(x) {
return(RandomName(length = 20))
}
)
placeholder.groups <- rep(x = levels(x = group.use), times = lines.width)
group.levels <- levels(x = group.use)
names(x = placeholder.groups) <- placeholder.cells
group.use <- as.vector(x = group.use)
names(x = group.use) <- cells
group.use <- factor(x = c(group.use, placeholder.groups), levels = group.levels)
na.data.group <- matrix(
data = NA,
nrow = length(x = placeholder.cells),
ncol = ncol(x = data.group),
dimnames = list(placeholder.cells, colnames(x = data.group))
)
data.group <- rbind(data.group, na.data.group)
}
lgroup <- length(levels(group.use))
plot <- SingleRasterMap(
data = data.group,
raster = raster,
disp.min = disp.min,
disp.max = disp.max,
feature.order = features,
cell.order = names(x = sort(x = group.use)),
group.by = group.use
)
if (group.bar) {
# TODO: Change group.bar to annotation.bar
default.colors <- c(hue_pal()(length(x = levels(x = group.use))))
if (!is.null(x = names(x = group.colors))) {
cols <- unname(obj = group.colors[levels(x = group.use)])
} else {
cols <- group.colors[1:length(x = levels(x = group.use))] %||% default.colors
}
if (any(is.na(x = cols))) {
cols[is.na(x = cols)] <- default.colors[is.na(x = cols)]
cols <- Col2Hex(cols)
col.dups <- sort(x = unique(x = which(x = duplicated(x = substr(
x = cols,
start = 1,
stop = 7
)))))
through <- length(x = default.colors)
while (length(x = col.dups) > 0) {
pal.max <- length(x = col.dups) + through
cols.extra <- hue_pal()(pal.max)[(through + 1):pal.max]
cols[col.dups] <- cols.extra
col.dups <- sort(x = unique(x = which(x = duplicated(x = substr(
x = cols,
start = 1,
stop = 7
)))))
}
}
group.use2 <- sort(x = group.use)
if (draw.lines) {
na.group <- RandomName(length = 20)
levels(x = group.use2) <- c(levels(x = group.use2), na.group)
group.use2[placeholder.cells] <- na.group
cols <- c(cols, "#FFFFFF")
}
pbuild <- ggplot_build(plot = plot)
names(x = cols) <- levels(x = group.use2)
# scale the height of the bar
y.range <- diff(x = pbuild$layout$panel_params[[1]]$y.range)
y.pos <- max(pbuild$layout$panel_params[[1]]$y.range) + y.range * 0.015
y.max <- y.pos + group.bar.height * y.range
x.min <- min(pbuild$layout$panel_params[[1]]$x.range) + 0.1
x.max <- max(pbuild$layout$panel_params[[1]]$x.range) - 0.1
plot <- plot +
annotation_raster(
raster = t(x = cols[group.use2]),
xmin = x.min,
xmax = x.max,
ymin = y.pos,
ymax = y.max
) +
coord_cartesian(ylim = c(0, y.max), clip = 'off') +
scale_color_manual(
values = cols[-length(x = cols)],
name = "Identity",
na.translate = FALSE
)
if (label) {
x.max <- max(pbuild$layout$panel_params[[1]]$x.range)
# Attempt to pull xdivs from x.major in ggplot2 < 3.3.0; if NULL, pull from the >= 3.3.0 slot
x.divs <- pbuild$layout$panel_params[[1]]$x.major %||% attr(x = pbuild$layout$panel_params[[1]]$x$get_breaks(), which = "pos")
x <- data.frame(group = sort(x = group.use), x = x.divs)
label.x.pos <- tapply(X = x$x, INDEX = x$group, FUN = function(y) {
if (isTRUE(x = draw.lines)) {
mean(x = y[-length(x = y)])
} else {
mean(x = y)
}
})
label.x.pos <- data.frame(group = names(x = label.x.pos), label.x.pos)
plot <- plot + geom_text(
stat = "identity",
data = label.x.pos,
aes_string(label = 'group', x = 'label.x.pos'),
y = y.max + y.max * 0.03 * 0.5 + vjust,
angle = angle,
hjust = hjust,
size = size
)
plot <- suppressMessages(plot + coord_cartesian(
ylim = c(0, y.max + y.max * 0.002 * max(nchar(x = levels(x = group.use))) * size),
clip = 'off')
)
}
}
plot <- plot + theme(line = element_blank())
plots[[i]] <- plot
}
if (combine) {
plots <- wrap_plots(plots)
}
return(plots)
}
#' Hashtag oligo heatmap
#'
#' Draws a heatmap of hashtag oligo signals across singlets/doublets/negative cells. Allows for the visualization of HTO demultiplexing results.
#'
#' @param object Seurat object. Assumes that the hash tag oligo (HTO) data has been added and normalized, and demultiplexing has been run with HTODemux().
#' @param classification The naming for metadata column with classification result from HTODemux().
#' @param global.classification The slot for metadata column specifying a cell as singlet/doublet/negative.
#' @param assay Hashtag assay name.
#' @param ncells Number of cells to plot. Default is to choose 5000 cells by random subsampling, to avoid having to draw exceptionally large heatmaps.
#' @param singlet.names Namings for the singlets. Default is to use the same names as HTOs.
#' @param raster If true, plot with geom_raster, else use geom_tile. geom_raster may look blurry on
#' some viewing applications such as Preview due to how the raster is interpolated. Set this to FALSE
#' if you are encountering that issue (note that plots may take longer to produce/render).
#' @return Returns a ggplot2 plot object.
#'
#' @importFrom ggplot2 guides
#' @export
#' @concept visualization
#'
#' @seealso \code{\link{HTODemux}}
#'
#' @examples
#' \dontrun{
#' object <- HTODemux(object)
#' HTOHeatmap(object)
#' }
#'
HTOHeatmap <- function(
object,
assay = 'HTO',
classification = paste0(assay, '_classification'),
global.classification = paste0(assay, '_classification.global'),
ncells = 5000,
singlet.names = NULL,
raster = TRUE
) {
DefaultAssay(object = object) <- assay
Idents(object = object) <- object[[classification, drop = TRUE]]
if (ncells > ncol(x = object)) {
warning("ncells (", ncells, ") is larger than the number of cells present in the provided object (", ncol(x = object), "). Plotting heatmap for all cells.")
} else {
object <- subset(
x = object,
cells = sample(x = colnames(x = object), size = ncells)
)
}
classification <- object[[classification]]
singlets <- which(x = object[[global.classification]] == 'Singlet')
singlet.ids <- sort(x = unique(x = as.character(x = classification[singlets, ])))
doublets <- which(object[[global.classification]] == 'Doublet')
doublet.ids <- sort(x = unique(x = as.character(x = classification[doublets, ])))
heatmap.levels <- c(singlet.ids, doublet.ids, 'Negative')
object <- ScaleData(object = object, assay = assay, verbose = FALSE)
data <- FetchData(object = object, vars = singlet.ids)
Idents(object = object) <- factor(x = classification[, 1], levels = heatmap.levels)
plot <- SingleRasterMap(
data = data,
raster = raster,
feature.order = rev(x = singlet.ids),
cell.order = names(x = sort(x = Idents(object = object))),
group.by = Idents(object = object)
) + guides(color = FALSE)
return(plot)
}
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Expression by identity plots
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#' Single cell ridge plot
#'
#' Draws a ridge plot of single cell data (gene expression, metrics, PC
#' scores, etc.)
#'
#' @param object Seurat object
#' @param features Features to plot (gene expression, metrics, PC scores,
#' anything that can be retreived by FetchData)
#' @param cols Colors to use for plotting
#' @param idents Which classes to include in the plot (default is all)
#' @param sort Sort identity classes (on the x-axis) by the average
#' expression of the attribute being potted, can also pass 'increasing' or 'decreasing' to change sort direction
#' @param assay Name of assay to use, defaults to the active assay
#' @param group.by Group (color) cells in different ways (for example, orig.ident)
#' @param y.max Maximum y axis value
#' @param same.y.lims Set all the y-axis limits to the same values
#' @param log plot the feature axis on log scale
#' @param ncol Number of columns if multiple plots are displayed
#' @param slot Slot to pull expression data from (e.g. "counts" or "data")
#' @param stack Horizontally stack plots for each feature
#' @param combine Combine plots into a single \code{\link[patchwork]{patchwork}ed}
#' ggplot object. If \code{FALSE}, return a list of ggplot
#' @param fill.by Color violins/ridges based on either 'feature' or 'ident'
#'
#' @return A \code{\link[patchwork]{patchwork}ed} ggplot object if
#' \code{combine = TRUE}; otherwise, a list of ggplot objects
#'
#' @export
#' @concept visualization
#'
#' @examples
#' data("pbmc_small")
#' RidgePlot(object = pbmc_small, features = 'PC_1')
#'
RidgePlot <- function(
object,
features,
cols = NULL,
idents = NULL,
sort = FALSE,
assay = NULL,
group.by = NULL,
y.max = NULL,
same.y.lims = FALSE,
log = FALSE,
ncol = NULL,
slot = deprecated(),
layer = 'data',
stack = FALSE,
combine = TRUE,
fill.by = 'feature'
) {
if (is_present(arg = slot)) {
deprecate_soft(
when = '5.0.0',
what = 'RidgePlot(slot = )',
with = 'RidgePlot(layer = )'
)
layer <- slot %||% layer
}
return(ExIPlot(
object = object,
type = 'ridge',
features = features,
idents = idents,
ncol = ncol,
sort = sort,
assay = assay,
y.max = y.max,
same.y.lims = same.y.lims,
cols = cols,
group.by = group.by,
log = log,
layer = layer,
stack = stack,
combine = combine,
fill.by = fill.by
))
}
#' Single cell violin plot
#'
#' Draws a violin plot of single cell data (gene expression, metrics, PC
#' scores, etc.)
#'
#' @inheritParams RidgePlot
#' @param pt.size Point size for points
#' @param alpha Alpha value for points
#' @param split.by A factor in object metadata to split the plot by, pass 'ident'
#' to split by cell identity'
#' @param split.plot plot each group of the split violin plots by multiple or
#' single violin shapes.
#' @param adjust Adjust parameter for geom_violin
#' @param flip flip plot orientation (identities on x-axis)
#' @param add.noise determine if adding a small noise for plotting
#' @param raster Convert points to raster format. Requires 'ggrastr' to be installed.
# default is \code{NULL} which automatically rasterizes if ggrastr is installed and
# number of points exceed 100,000.
#'
#' @return A \code{\link[patchwork]{patchwork}ed} ggplot object if
#' \code{combine = TRUE}; otherwise, a list of ggplot objects
#'
#' @export
#' @concept visualization
#'
#' @seealso \code{\link{FetchData}}
#'
#' @examples
#' data("pbmc_small")
#' VlnPlot(object = pbmc_small, features = 'PC_1')
#' VlnPlot(object = pbmc_small, features = 'LYZ', split.by = 'groups')
#'
VlnPlot <- function(
object,
features,
cols = NULL,
pt.size = NULL,
alpha = 1,
idents = NULL,
sort = FALSE,
assay = NULL,
group.by = NULL,
split.by = NULL,
adjust = 1,
y.max = NULL,
same.y.lims = FALSE,
log = FALSE,
ncol = NULL,
slot = deprecated(),
layer = 'data',
split.plot = FALSE,
stack = FALSE,
combine = TRUE,
fill.by = 'feature',
flip = FALSE,
add.noise = TRUE,
raster = NULL
) {
if (is_present(arg = slot)) {
deprecate_soft(
when = '5.0.0',
what = 'VlnPlot(slot = )',
with = 'VlnPlot(layer = )'
)
layer <- slot %||% layer
}
if (
!is.null(x = split.by) &
getOption(x = 'Seurat.warn.vlnplot.split', default = TRUE)
) {
message(
"The default behaviour of split.by has changed.\n",
"Separate violin plots are now plotted side-by-side.\n",
"To restore the old behaviour of a single split violin,\n",
"set split.plot = TRUE.
\nThis message will be shown once per session."
)
options(Seurat.warn.vlnplot.split = FALSE)
}
return(ExIPlot(
object = object,
type = ifelse(test = split.plot, yes = 'splitViolin', no = 'violin'),
features = features,
idents = idents,
ncol = ncol,
sort = sort,
assay = assay,
y.max = y.max,
same.y.lims = same.y.lims,
adjust = adjust,
pt.size = pt.size,
alpha = alpha,
cols = cols,
group.by = group.by,
split.by = split.by,
log = log,
layer = layer,
stack = stack,
combine = combine,
fill.by = fill.by,
flip = flip,
add.noise = add.noise,
raster = raster
))
}
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Dimensional reduction plots
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#' Color dimensional reduction plot by tree split
#'
#' Returns a DimPlot colored based on whether the cells fall in clusters
#' to the left or to the right of a node split in the cluster tree.
#'
#' @param object Seurat object
#' @param node Node in cluster tree on which to base the split
#' @param left.color Color for the left side of the split
#' @param right.color Color for the right side of the split
#' @param other.color Color for all other cells
#' @inheritDotParams DimPlot -object
#'
#' @return Returns a DimPlot
#'
#' @export
#' @concept visualization
#'
#' @seealso \code{\link{DimPlot}}
#'
#' @examples
#' if (requireNamespace("ape", quietly = TRUE)) {
#' data("pbmc_small")
#' pbmc_small <- BuildClusterTree(object = pbmc_small, verbose = FALSE)
#' PlotClusterTree(pbmc_small)
#' ColorDimSplit(pbmc_small, node = 5)
#' }
#'
ColorDimSplit <- function(
object,
node,
left.color = 'red',
right.color = 'blue',
other.color = 'grey50',
...
) {
CheckDots(..., fxns = 'DimPlot')
tree <- Tool(object = object, slot = "BuildClusterTree")
split <- tree$edge[which(x = tree$edge[, 1] == node), ][, 2]
all.children <- sort(x = tree$edge[, 2][!tree$edge[, 2] %in% tree$edge[, 1]])
left.group <- DFT(tree = tree, node = split[1], only.children = TRUE)
right.group <- DFT(tree = tree, node = split[2], only.children = TRUE)
if (any(is.na(x = left.group))) {
left.group <- split[1]
}
if (any(is.na(x = right.group))) {
right.group <- split[2]
}
left.group <- MapVals(v = left.group, from = all.children, to = tree$tip.label)
right.group <- MapVals(v = right.group, from = all.children, to = tree$tip.label)
remaining.group <- setdiff(x = tree$tip.label, y = c(left.group, right.group))
left.cells <- WhichCells(object = object, ident = left.group)
right.cells <- WhichCells(object = object, ident = right.group)
remaining.cells <- WhichCells(object = object, ident = remaining.group)
object <- SetIdent(
object = object,
cells = left.cells,
value = "Left Split"
)
object <- SetIdent(
object = object,
cells = right.cells,
value = "Right Split"
)
object <- SetIdent(
object = object,
cells = remaining.cells,
value = "Not in Split"
)
levels(x = object) <- c("Left Split", "Right Split", "Not in Split")
colors.use = c(left.color, right.color, other.color)
return(DimPlot(object = object, cols = colors.use, ...))
}
#' Dimensional reduction plot
#'
#' Graphs the output of a dimensional reduction technique on a 2D scatter plot where each point is a
#' cell and it's positioned based on the cell embeddings determined by the reduction technique. By
#' default, cells are colored by their identity class (can be changed with the group.by parameter).
#'
#' @param object Seurat object
#' @param dims Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions
#' @param cells Vector of cells to plot (default is all cells)
#' @param cols Vector of colors, each color corresponds to an identity class. This may also be a single character
#' or numeric value corresponding to a palette as specified by \code{\link[RColorBrewer]{brewer.pal.info}}.
#' By default, ggplot2 assigns colors. We also include a number of palettes from the pals package.
#' See \code{\link{DiscretePalette}} for details.
#' @param pt.size Adjust point size for plotting
#' @param reduction Which dimensionality reduction to use. If not specified, first searches for umap, then tsne, then pca
#' @param group.by Name of one or more metadata columns to group (color) cells by
#' (for example, orig.ident); pass 'ident' to group by identity class
#' @param split.by A factor in object metadata to split the plot by, pass 'ident'
#' to split by cell identity'
#' @param shape.by If NULL, all points are circles (default). You can specify any
#' cell attribute (that can be pulled with FetchData) allowing for both
#' different colors and different shapes on cells. Only applicable if \code{raster = FALSE}.
#' @param order Specify the order of plotting for the idents. This can be
#' useful for crowded plots if points of interest are being buried. Provide
#' either a full list of valid idents or a subset to be plotted last (on top)
#' @param shuffle Whether to randomly shuffle the order of points. This can be
#' useful for crowded plots if points of interest are being buried. (default is FALSE)
#' @param seed Sets the seed if randomly shuffling the order of points.
#' @param label Whether to label the clusters
#' @param label.size Sets size of labels
#' @param label.color Sets the color of the label text
#' @param label.box Whether to put a box around the label text (geom_text vs
#' geom_label)
#' @param alpha Alpha value for plotting (default is 1)
#' @param repel Repel labels
#' @param cells.highlight A list of character or numeric vectors of cells to
#' highlight. If only one group of cells desired, can simply
#' pass a vector instead of a list. If set, colors selected cells to the color(s)
#' in \code{cols.highlight} and other cells black (white if dark.theme = TRUE);
#' will also resize to the size(s) passed to \code{sizes.highlight}
#' @param cols.highlight A vector of colors to highlight the cells as; will
#' repeat to the length groups in cells.highlight
#' @param sizes.highlight Size of highlighted cells; will repeat to the length
#' groups in cells.highlight
#' @param na.value Color value for NA points when using custom scale
#' @param ncol Number of columns for display when combining plots
#' @param combine Combine plots into a single \code{\link[patchwork]{patchwork}ed}
#' ggplot object. If \code{FALSE}, return a list of ggplot objects
#' @param raster Convert points to raster format, default is \code{NULL} which
#' automatically rasterizes if plotting more than 100,000 cells
#' @param raster.dpi Pixel resolution for rasterized plots, passed to geom_scattermore().
#' Default is c(512, 512).
#'
#' @return A \code{\link[patchwork]{patchwork}ed} ggplot object if
#' \code{combine = TRUE}; otherwise, a list of ggplot objects
#'
#' @importFrom rlang !!
#' @importFrom ggplot2 facet_wrap vars sym labs
#' @importFrom patchwork wrap_plots
#'
#' @export
#' @concept visualization
#'
#' @note For the old \code{do.hover} and \code{do.identify} functionality, please see
#' \code{HoverLocator} and \code{CellSelector}, respectively.
#'
#' @aliases TSNEPlot PCAPlot ICAPlot
#' @seealso \code{\link{FeaturePlot}} \code{\link{HoverLocator}}
#' \code{\link{CellSelector}} \code{\link{FetchData}}
#'
#' @examples
#' data("pbmc_small")
#' DimPlot(object = pbmc_small)
#' DimPlot(object = pbmc_small, split.by = 'ident')
#'
DimPlot <- function(
object,
dims = c(1, 2),
cells = NULL,
cols = NULL,
pt.size = NULL,
reduction = NULL,
group.by = NULL,
split.by = NULL,
shape.by = NULL,
order = NULL,
shuffle = FALSE,
seed = 1,
label = FALSE,
label.size = 4,
label.color = 'black',
label.box = FALSE,
repel = FALSE,
alpha = 1,
cells.highlight = NULL,
cols.highlight = '#DE2D26',
sizes.highlight = 1,
na.value = 'grey50',
ncol = NULL,
combine = TRUE,
raster = NULL,
raster.dpi = c(512, 512)
) {
if (!is_integerish(x = dims, n = 2L, finite = TRUE) || !all(dims > 0L)) {
abort(message = "'dims' must be a two-length integer vector")
}
reduction <- reduction %||% DefaultDimReduc(object = object)
# cells <- cells %||% colnames(x = object)
##### Cells for all cells in the assay.
#### Cells function should not only get default layer
cells <- cells %||% Cells(
x = object,
assay = DefaultAssay(object = object[[reduction]])
)
# data <- Embeddings(object = object[[reduction]])[cells, dims]
# data <- as.data.frame(x = data)
dims <- paste0(Key(object = object[[reduction]]), dims)
orig.groups <- group.by
group.by <- group.by %||% 'ident'
data <- FetchData(
object = object,
vars = c(dims, group.by),
cells = cells,
clean = 'project'
)
# cells <- rownames(x = object)
# object[['ident']] <- Idents(object = object)
# orig.groups <- group.by
# group.by <- group.by %||% 'ident'
# data <- cbind(data, object[[group.by]][cells, , drop = FALSE])
group.by <- colnames(x = data)[3:ncol(x = data)]
for (group in group.by) {
if (!is.factor(x = data[, group])) {
data[, group] <- factor(x = data[, group])
}
}
if (!is.null(x = shape.by)) {
data[, shape.by] <- object[[shape.by, drop = TRUE]]
}
if (!is.null(x = split.by)) {
data[, split.by] <- FetchData(object,split.by)[split.by]
}
if (isTRUE(x = shuffle)) {
set.seed(seed = seed)
data <- data[sample(x = 1:nrow(x = data)), ]
}
plots <- lapply(
X = group.by,
FUN = function(x) {
plot <- SingleDimPlot(
data = data[, c(dims, x, split.by, shape.by)],
dims = dims,
col.by = x,
cols = cols,
pt.size = pt.size,
shape.by = shape.by,
order = order,
alpha = alpha,
label = FALSE,
cells.highlight = cells.highlight,
cols.highlight = cols.highlight,
sizes.highlight = sizes.highlight,
na.value = na.value,
raster = raster,
raster.dpi = raster.dpi
)
if (label) {
plot <- LabelClusters(
plot = plot,
id = x,
repel = repel,
size = label.size,
split.by = split.by,
box = label.box,
color = label.color
)
}
if (!is.null(x = split.by)) {
plot <- plot + FacetTheme() +
facet_wrap(
facets = vars(!!sym(x = split.by)),
ncol = if (length(x = group.by) > 1 || is.null(x = ncol)) {
length(x = unique(x = data[, split.by]))
} else {
ncol
}
)
}
plot <- if (is.null(x = orig.groups)) {
plot + labs(title = NULL)
} else {
plot + CenterTitle()
}
}
)
if (!is.null(x = split.by)) {
ncol <- 1
}
if (combine) {
plots <- wrap_plots(plots, ncol = orig.groups %iff% ncol)
}
return(plots)
}
#' Visualize 'features' on a dimensional reduction plot
#'
#' Colors single cells on a dimensional reduction plot according to a 'feature'
#' (i.e. gene expression, PC scores, number of genes detected, etc.)
#'
#' @inheritParams DimPlot
#' @param order Boolean determining whether to plot cells in order of expression. Can be useful if
#' cells expressing given feature are getting buried.
#' @param features Vector of features to plot. Features can come from:
#' \itemize{
#' \item An \code{Assay} feature (e.g. a gene name - "MS4A1")
#' \item A column name from meta.data (e.g. mitochondrial percentage - "percent.mito")
#' \item A column name from a \code{DimReduc} object corresponding to the cell embedding values
#' (e.g. the PC 1 scores - "PC_1")
#' }
#' @param cols The two colors to form the gradient over. Provide as string vector with
#' the first color corresponding to low values, the second to high. Also accepts a Brewer
#' color scale or vector of colors. Note: this will bin the data into number of colors provided.
#' When blend is \code{TRUE}, takes anywhere from 1-3 colors:
#' \describe{
#' \item{1 color:}{Treated as color for double-negatives, will use default colors 2 and 3 for per-feature expression}
#' \item{2 colors:}{Treated as colors for per-feature expression, will use default color 1 for double-negatives}
#' \item{3+ colors:}{First color used for double-negatives, colors 2 and 3 used for per-feature expression, all others ignored}
#' }
#' @param min.cutoff,max.cutoff Vector of minimum and maximum cutoff values for each feature,
#' may specify quantile in the form of 'q##' where '##' is the quantile (eg, 'q1', 'q10')
#' @param split.by A factor in object metadata to split the plot by, pass 'ident'
#' to split by cell identity'
#' @param keep.scale How to handle the color scale across multiple plots. Options are:
#' \itemize{
#' \item{"feature" (default; by row/feature scaling):}{ The plots for each individual feature are scaled to the maximum expression of the feature across the conditions provided to 'split.by'.}
#' \item{"all" (universal scaling):}{ The plots for all features and conditions are scaled to the maximum expression value for the feature with the highest overall expression.}
#' \item{NULL (no scaling):}{ Each individual plot is scaled to the maximum expression value of the feature in the condition provided to 'split.by'. Be aware setting NULL will result in color scales that are not comparable between plots.}
#' }
#' @param slot Which slot to pull expression data from?
#' @param blend Scale and blend expression values to visualize coexpression of two features
#' @param blend.threshold The color cutoff from weak signal to strong signal; ranges from 0 to 1.
#' @param ncol Number of columns to combine multiple feature plots to, ignored if \code{split.by} is not \code{NULL}
#' @param coord.fixed Plot cartesian coordinates with fixed aspect ratio
#' @param by.col If splitting by a factor, plot the splits per column with the features as rows; ignored if \code{blend = TRUE}