R/plotHeatmap.R
In davismcc/scater: Single-Cell Analysis Toolkit for Gene Expression Data in R
Defines functions
.heatmap_scale
plotHeatmap
Documented in
plotHeatmap
#' Plot heatmap of gene expression values
#'
#' Create a heatmap of expression values for each cell and specified features in a SingleCellExperiment object.
#'
#' @param object A \linkS4class{SingleCellExperiment} object.
#' @param features A character (or factor) vector of row names, a logical vector, or integer vector of indices specifying rows of \code{object} to visualize. When using character or integer vectors, the ordering specified by the user is retained. When using factor vectors, ordering is controlled by the factor levels.
#' @param columns A vector specifying the subset of columns in \code{object} to show as columns in the heatmap.
#' Also specifies the column order if \code{cluster_cols=FALSE} and \code{order_columns_by=NULL}.
#' By default, all columns are used.
#' @param assay.type A string or integer scalar indicating which assay of \code{object} should be used as expression values.
#' @param center A logical scalar indicating whether each feature should have its mean expression centered at zero prior to plotting.
#' @param scale A logical scalar specifying whether each feature should have its expression values scaled to have unit variance prior to plotting.
#' @param zlim A numeric vector of length 2, specifying the upper and lower bounds for colour mapping of expression values.
#' Values outside this range are set to the most extreme colour.
#' If \code{NULL}, it defaults to the range of the expression matrix.
#' If \code{center=TRUE}, this defaults to the range of the centered expression matrix, made symmetric around zero.
#' @param colour A vector of colours specifying the palette to use for increasing expression.
#' This defaults to \link[viridis]{viridis} if \code{center=FALSE}, and the the \code{"RdYlBu"}
#' colour palette from \code{\link[RColorBrewer]{brewer.pal}} otherwise.
#' @param colour_columns_by A list of values specifying how the columns should be annotated with colours.
#' Each entry of the list can be any acceptable input to the \code{by} argument in \code{?\link{retrieveCellInfo}}.
#' A character vector can also be supplied and will be treated as a list of strings.
#' @param column_annotation_colours A named list of colour scales to be used for
#' the column annotations specified in \code{colour_columns_by}. Names
#' should be character values present in \code{colour_columns_by},
#' If a colour scale is not specified for a particular annotation, a default
#' colour scale is chosen.
#' The full list of colour maps is passed to \code{\link[pheatmap]{pheatmap}}
#' as the \code{annotation_colours} argument.
#' @param colour_rows_by Similar to \code{colour_columns_by} but for rows rather
#' than columns. Each entry of the list can be any acceptable input to the
#' \code{by} argument in \code{?\link{retrieveFeatureInfo}}.
#' @param row_annotation_colours Similar to \code{column_annotation_colours} but
#' relating to row annotation rather than column annotation.
#' @param order_columns_by A list of values specifying how the columns should be ordered.
#' Each entry of the list can be any acceptable input to the \code{by} argument in \code{?\link{retrieveCellInfo}}.
#' A character vector can also be supplied and will be treated as a list of strings.
#' This argument is automatically appended to \code{colour_columns_by}.
#' @param by.assay.type A string or integer scalar specifying which assay to obtain expression values from,
#' for colouring of column-level data - see the \code{assay.type} argument in \code{?\link{retrieveCellInfo}}.
#' @param show_colnames,cluster_cols,... Additional arguments to pass to \code{\link[pheatmap]{pheatmap}}.
#' @param swap_rownames Column name of \code{rowData(object)} to be used to
#' identify features instead of \code{rownames(object)} when labelling plot
#' elements.
#' @param color,color_columns_by,column_annotation_colors,color_rows_by,row_annotation_colors
#' Aliases to \code{color}, \code{color_columns_by},
#' \code{column_annotation_colors}, \code{color_rows_by},
#' \code{row_annotation_colors}.
#' @param exprs_values Alias to \code{assay.type}.
#' @param by_exprs_values Alias to {by.assay.type}.
#'
#' @details
#' Setting \code{center=TRUE} is useful for examining log-fold changes of each cell's expression profile from the average across all cells.
#' This avoids issues with the entire row appearing a certain colour because the gene is highly/lowly expressed across all cells.
#'
#' Setting \code{zlim} preserves the dynamic range of colours in the presence of outliers.
#' Otherwise, the plot may be dominated by a few genes, which will \dQuote{flatten} the observed colours for the rest of the heatmap.
#'
#' Setting \code{order_columns_by} is useful for automatically ordering the heatmap by one or more factors of interest, e.g., cluster identity.
#' This avoids the need to set \code{colour_columns_by}, \code{cluster_cols} and \code{columns} to achieve the same effect.
#'
#' @return A heatmap is produced on the current graphics device.
#' The output of \code{\link[pheatmap]{pheatmap}} is invisibly returned.
#'
#' @seealso \code{\link[pheatmap]{pheatmap}}
#'
#' @author Aaron Lun
#'
#' @examples
#' example_sce <- mockSCE()
#' example_sce <- logNormCounts(example_sce)
#'
#' plotHeatmap(example_sce, features=rownames(example_sce)[1:10])
#'
#' plotHeatmap(example_sce, features=rownames(example_sce)[1:10],
#' center=TRUE)
#'
#' plotHeatmap(example_sce, features=rownames(example_sce)[1:10],
#' colour_columns_by=c("Mutation_Status", "Cell_Cycle"))
#'
#' @export
#' @importFrom DelayedArray DelayedArray
#' @importFrom MatrixGenerics rowMeans2
#' @importFrom viridis viridis
#' @importFrom SummarizedExperiment assay assayNames
plotHeatmap <- function(object, features, columns = NULL,
exprs_values = "logcounts", center = FALSE, scale = FALSE, zlim = NULL,
colour = color, color = NULL,
colour_columns_by = color_columns_by,
color_columns_by = NULL,
column_annotation_colours = column_annotation_colors,
column_annotation_colors = list(),
row_annotation_colours = row_annotation_colors,
row_annotation_colors = list(),
colour_rows_by = color_rows_by,
color_rows_by = NULL,
order_columns_by = NULL, by_exprs_values = exprs_values,
show_colnames = FALSE, cluster_cols = is.null(order_columns_by),
swap_rownames = NULL,
assay.type=exprs_values,
by.assay.type=by_exprs_values,
...) {
# Setting names, otherwise the downstream colouring fails.
if (is.null(colnames(object))) {
colnames(object) <- seq_len(ncol(object))
}
# Pulling out the features. swap_rownames swaps out for alt genenames
object <- .swap_rownames(object, swap_rownames)
# in case of numeric or logical features, converts to character or factor
features <- .handle_features(features, object)
heat.vals <- assay(object, assay.type)[as.character(features), , drop=FALSE]
if (is.factor(features)) {
heat.vals <- heat.vals[levels(features), , drop = FALSE]
}
if (!is.null(columns)) {
columns <- .subset2index(columns, object, byrow=FALSE)
heat.vals <- heat.vals[, columns, drop=FALSE]
}
if (!is.null(order_columns_by)) {
ordering <- list()
for (i in seq_along(order_columns_by)) {
vals <- retrieveCellInfo(object, order_columns_by[[i]], assay.type = by.assay.type)$value
if (!is.null(columns)) {
vals <- vals[columns]
}
ordering[[i]] <- vals
}
heat.vals <- heat.vals[,do.call(order, ordering),drop=FALSE]
cluster_cols <- FALSE
colour_columns_by <- c(colour_columns_by, order_columns_by)
}
heatmap_scale <- .heatmap_scale(heat.vals, center=center, scale=scale, colour=colour, zlim=zlim)
# Collecting variables to colour_by.
if (length(colour_columns_by)) {
column_variables <- list()
for (i in seq_along(colour_columns_by)) {
field <- colour_columns_by[[i]]
colour_by_out <- retrieveCellInfo(object, field,
assay.type = by.assay.type, swap_rownames = swap_rownames)
if (is.null(colour_by_out$value)) {
next
} else if (is.numeric(colour_by_out$value)) {
colour_fac <- colour_by_out$value
col_scale <- viridis(25)
} else {
colour_fac <- as.factor(colour_by_out$value)
nlevs_colour_by <- nlevels(colour_fac)
if (nlevs_colour_by <= 10) {
col_scale <- .get_palette("tableau10medium")
} else if (nlevs_colour_by > 10 && nlevs_colour_by <= 20) {
col_scale <- .get_palette("tableau20")
} else {
col_scale <- viridis(nlevs_colour_by)
}
col_scale <- col_scale[seq_len(nlevs_colour_by)]
names(col_scale) <- levels(colour_fac)
}
col_name <- colour_by_out$name
if (col_name == "") {
col_name <- paste0("unnamed", i)
}
column_variables[[col_name]] <- colour_fac
if (is.null(column_annotation_colours[[col_name]])) {
column_annotation_colours[[col_name]] <- col_scale
}
}
# No need to subset for 'columns' or 'order_columns_by',
# as pheatmap::pheatmap uses the rownames to handle this for us.
column_variables <- do.call(data.frame,
c(column_variables, list(row.names = colnames(object))))
column_annotation_colours <- column_annotation_colours[colnames(column_variables)]
} else {
column_variables <- column_annotation_colours <- NULL
}
if (length(colour_rows_by)) {
row_variables <- list()
for (i in seq_along(colour_rows_by)) {
field <- colour_rows_by[[i]]
colour_by_out <- retrieveFeatureInfo(object, field,
assay.type = by.assay.type)
if (is.null(colour_by_out$value)) {
next
} else if (is.numeric(colour_by_out$value)) {
colour_fac <- colour_by_out$value
col_scale <- viridis(25)
} else {
colour_fac <- as.factor(colour_by_out$value)
nlevs_colour_by <- nlevels(colour_fac)
if (nlevs_colour_by <= 10) {
col_scale <- .get_palette("tableau10medium")
} else if (nlevs_colour_by > 10 && nlevs_colour_by <= 20) {
col_scale <- .get_palette("tableau20")
} else {
col_scale <- viridis(nlevs_colour_by)
}
col_scale <- col_scale[seq_len(nlevs_colour_by)]
names(col_scale) <- levels(colour_fac)
}
col_name <- colour_by_out$name
if (col_name == "") {
col_name <- paste0("unnamed", i)
}
row_variables[[col_name]] <- colour_fac
if (is.null(row_annotation_colours[[col_name]])) {
row_annotation_colours[[col_name]] <- col_scale
}
}
row_variables <- do.call(
data.frame,
c(row_variables, list(row.names = rownames(object)))
)
row_annotation_colours <- row_annotation_colours[colnames(row_variables)]
} else {
row_variables <- row_annotation_colours <- NULL
}
if (length(intersect(names(row_annotation_colours), names(column_annotation_colours)))) {
warning("Element with the same name in row and column annotations. ",
"Assuming they're the same.")
}
annotation_colours <- c(row_annotation_colours, column_annotation_colours)
# Creating the heatmap as specified.
pheatmap::pheatmap(
heatmap_scale$x,
color = heatmap_scale$colour,
breaks = heatmap_scale$colour_breaks,
annotation_col = column_variables,
annotation_row = row_variables,
annotation_colors = annotation_colours,
show_colnames = show_colnames,
cluster_cols = cluster_cols,
...
)
}
#' @importFrom ggplot2 scale_colour_gradientn
.heatmap_scale <- function(x, center, scale, colour=NULL, zlim=NULL, symmetric=NULL) {
if (center) {
x <- x - rowMeans(x)
}
if (scale) {
if (!center & any(rowSums(x) == 0)) {
stop("Cannot include non-expressed genes when scale=TRUE.")
}
x <- x / sqrt(rowSums(x^2) / (ncol(x) - 1))
}
if (is.null(zlim)) {
if (center) {
extreme <- max(abs(x))
zlim <- c(-extreme, extreme)
} else {
zlim <- range(x)
}
}
if (is.null(colour)) {
if (center) {
colour <- rev(RColorBrewer::brewer.pal(9, "RdYlBu"))
} else {
colour <- viridis::viridis(9)
}
}
x[x < zlim[1]] <- zlim[1]
x[x > zlim[2]] <- zlim[2]
list(
x = x,
colour = colour,
colour_breaks = seq(zlim[1], zlim[2], length.out=length(colour) + 1L),
colour_scale = scale_colour_gradientn(colours = colour, limits = zlim),
zlim = zlim
)
}
davismcc/scater documentation built on Feb. 10, 2024, 10:53 a.m.
R Package Documentation
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Defines functions .heatmap_scale plotHeatmap
Documented in plotHeatmap
#' Plot heatmap of gene expression values
#'
#' Create a heatmap of expression values for each cell and specified features in a SingleCellExperiment object.
#'
#' @param object A \linkS4class{SingleCellExperiment} object.
#' @param features A character (or factor) vector of row names, a logical vector, or integer vector of indices specifying rows of \code{object} to visualize. When using character or integer vectors, the ordering specified by the user is retained. When using factor vectors, ordering is controlled by the factor levels.
#' @param columns A vector specifying the subset of columns in \code{object} to show as columns in the heatmap.
#' Also specifies the column order if \code{cluster_cols=FALSE} and \code{order_columns_by=NULL}.
#' By default, all columns are used.
#' @param assay.type A string or integer scalar indicating which assay of \code{object} should be used as expression values.
#' @param center A logical scalar indicating whether each feature should have its mean expression centered at zero prior to plotting.
#' @param scale A logical scalar specifying whether each feature should have its expression values scaled to have unit variance prior to plotting.
#' @param zlim A numeric vector of length 2, specifying the upper and lower bounds for colour mapping of expression values.
#' Values outside this range are set to the most extreme colour.
#' If \code{NULL}, it defaults to the range of the expression matrix.
#' If \code{center=TRUE}, this defaults to the range of the centered expression matrix, made symmetric around zero.
#' @param colour A vector of colours specifying the palette to use for increasing expression.
#' This defaults to \link[viridis]{viridis} if \code{center=FALSE}, and the the \code{"RdYlBu"}
#' colour palette from \code{\link[RColorBrewer]{brewer.pal}} otherwise.
#' @param colour_columns_by A list of values specifying how the columns should be annotated with colours.
#' Each entry of the list can be any acceptable input to the \code{by} argument in \code{?\link{retrieveCellInfo}}.
#' A character vector can also be supplied and will be treated as a list of strings.
#' @param column_annotation_colours A named list of colour scales to be used for
#' the column annotations specified in \code{colour_columns_by}. Names
#' should be character values present in \code{colour_columns_by},
#' If a colour scale is not specified for a particular annotation, a default
#' colour scale is chosen.
#' The full list of colour maps is passed to \code{\link[pheatmap]{pheatmap}}
#' as the \code{annotation_colours} argument.
#' @param colour_rows_by Similar to \code{colour_columns_by} but for rows rather
#' than columns. Each entry of the list can be any acceptable input to the
#' \code{by} argument in \code{?\link{retrieveFeatureInfo}}.
#' @param row_annotation_colours Similar to \code{column_annotation_colours} but
#' relating to row annotation rather than column annotation.
#' @param order_columns_by A list of values specifying how the columns should be ordered.
#' Each entry of the list can be any acceptable input to the \code{by} argument in \code{?\link{retrieveCellInfo}}.
#' A character vector can also be supplied and will be treated as a list of strings.
#' This argument is automatically appended to \code{colour_columns_by}.
#' @param by.assay.type A string or integer scalar specifying which assay to obtain expression values from,
#' for colouring of column-level data - see the \code{assay.type} argument in \code{?\link{retrieveCellInfo}}.
#' @param show_colnames,cluster_cols,... Additional arguments to pass to \code{\link[pheatmap]{pheatmap}}.
#' @param swap_rownames Column name of \code{rowData(object)} to be used to
#' identify features instead of \code{rownames(object)} when labelling plot
#' elements.
#' @param color,color_columns_by,column_annotation_colors,color_rows_by,row_annotation_colors
#' Aliases to \code{color}, \code{color_columns_by},
#' \code{column_annotation_colors}, \code{color_rows_by},
#' \code{row_annotation_colors}.
#' @param exprs_values Alias to \code{assay.type}.
#' @param by_exprs_values Alias to {by.assay.type}.
#'
#' @details
#' Setting \code{center=TRUE} is useful for examining log-fold changes of each cell's expression profile from the average across all cells.
#' This avoids issues with the entire row appearing a certain colour because the gene is highly/lowly expressed across all cells.
#'
#' Setting \code{zlim} preserves the dynamic range of colours in the presence of outliers.
#' Otherwise, the plot may be dominated by a few genes, which will \dQuote{flatten} the observed colours for the rest of the heatmap.
#'
#' Setting \code{order_columns_by} is useful for automatically ordering the heatmap by one or more factors of interest, e.g., cluster identity.
#' This avoids the need to set \code{colour_columns_by}, \code{cluster_cols} and \code{columns} to achieve the same effect.
#'
#' @return A heatmap is produced on the current graphics device.
#' The output of \code{\link[pheatmap]{pheatmap}} is invisibly returned.
#'
#' @seealso \code{\link[pheatmap]{pheatmap}}
#'
#' @author Aaron Lun
#'
#' @examples
#' example_sce <- mockSCE()
#' example_sce <- logNormCounts(example_sce)
#'
#' plotHeatmap(example_sce, features=rownames(example_sce)[1:10])
#'
#' plotHeatmap(example_sce, features=rownames(example_sce)[1:10],
#' center=TRUE)
#'
#' plotHeatmap(example_sce, features=rownames(example_sce)[1:10],
#' colour_columns_by=c("Mutation_Status", "Cell_Cycle"))
#'
#' @export
#' @importFrom DelayedArray DelayedArray
#' @importFrom MatrixGenerics rowMeans2
#' @importFrom viridis viridis
#' @importFrom SummarizedExperiment assay assayNames
plotHeatmap <- function(object, features, columns = NULL,
exprs_values = "logcounts", center = FALSE, scale = FALSE, zlim = NULL,
colour = color, color = NULL,
colour_columns_by = color_columns_by,
color_columns_by = NULL,
column_annotation_colours = column_annotation_colors,
column_annotation_colors = list(),
row_annotation_colours = row_annotation_colors,
row_annotation_colors = list(),
colour_rows_by = color_rows_by,
color_rows_by = NULL,
order_columns_by = NULL, by_exprs_values = exprs_values,
show_colnames = FALSE, cluster_cols = is.null(order_columns_by),
swap_rownames = NULL,
assay.type=exprs_values,
by.assay.type=by_exprs_values,
...) {
# Setting names, otherwise the downstream colouring fails.
if (is.null(colnames(object))) {
colnames(object) <- seq_len(ncol(object))
}
# Pulling out the features. swap_rownames swaps out for alt genenames
object <- .swap_rownames(object, swap_rownames)
# in case of numeric or logical features, converts to character or factor
features <- .handle_features(features, object)
heat.vals <- assay(object, assay.type)[as.character(features), , drop=FALSE]
if (is.factor(features)) {
heat.vals <- heat.vals[levels(features), , drop = FALSE]
}
if (!is.null(columns)) {
columns <- .subset2index(columns, object, byrow=FALSE)
heat.vals <- heat.vals[, columns, drop=FALSE]
}
if (!is.null(order_columns_by)) {
ordering <- list()
for (i in seq_along(order_columns_by)) {
vals <- retrieveCellInfo(object, order_columns_by[[i]], assay.type = by.assay.type)$value
if (!is.null(columns)) {
vals <- vals[columns]
}
ordering[[i]] <- vals
}
heat.vals <- heat.vals[,do.call(order, ordering),drop=FALSE]
cluster_cols <- FALSE
colour_columns_by <- c(colour_columns_by, order_columns_by)
}
heatmap_scale <- .heatmap_scale(heat.vals, center=center, scale=scale, colour=colour, zlim=zlim)
# Collecting variables to colour_by.
if (length(colour_columns_by)) {
column_variables <- list()
for (i in seq_along(colour_columns_by)) {
field <- colour_columns_by[[i]]
colour_by_out <- retrieveCellInfo(object, field,
assay.type = by.assay.type, swap_rownames = swap_rownames)
if (is.null(colour_by_out$value)) {
next
} else if (is.numeric(colour_by_out$value)) {
colour_fac <- colour_by_out$value
col_scale <- viridis(25)
} else {
colour_fac <- as.factor(colour_by_out$value)
nlevs_colour_by <- nlevels(colour_fac)
if (nlevs_colour_by <= 10) {
col_scale <- .get_palette("tableau10medium")
} else if (nlevs_colour_by > 10 && nlevs_colour_by <= 20) {
col_scale <- .get_palette("tableau20")
} else {
col_scale <- viridis(nlevs_colour_by)
}
col_scale <- col_scale[seq_len(nlevs_colour_by)]
names(col_scale) <- levels(colour_fac)
}
col_name <- colour_by_out$name
if (col_name == "") {
col_name <- paste0("unnamed", i)
}
column_variables[[col_name]] <- colour_fac
if (is.null(column_annotation_colours[[col_name]])) {
column_annotation_colours[[col_name]] <- col_scale
}
}
# No need to subset for 'columns' or 'order_columns_by',
# as pheatmap::pheatmap uses the rownames to handle this for us.
column_variables <- do.call(data.frame,
c(column_variables, list(row.names = colnames(object))))
column_annotation_colours <- column_annotation_colours[colnames(column_variables)]
} else {
column_variables <- column_annotation_colours <- NULL
}
if (length(colour_rows_by)) {
row_variables <- list()
for (i in seq_along(colour_rows_by)) {
field <- colour_rows_by[[i]]
colour_by_out <- retrieveFeatureInfo(object, field,
assay.type = by.assay.type)
if (is.null(colour_by_out$value)) {
next
} else if (is.numeric(colour_by_out$value)) {
colour_fac <- colour_by_out$value
col_scale <- viridis(25)
} else {
colour_fac <- as.factor(colour_by_out$value)
nlevs_colour_by <- nlevels(colour_fac)
if (nlevs_colour_by <= 10) {
col_scale <- .get_palette("tableau10medium")
} else if (nlevs_colour_by > 10 && nlevs_colour_by <= 20) {
col_scale <- .get_palette("tableau20")
} else {
col_scale <- viridis(nlevs_colour_by)
}
col_scale <- col_scale[seq_len(nlevs_colour_by)]
names(col_scale) <- levels(colour_fac)
}
col_name <- colour_by_out$name
if (col_name == "") {
col_name <- paste0("unnamed", i)
}
row_variables[[col_name]] <- colour_fac
if (is.null(row_annotation_colours[[col_name]])) {
row_annotation_colours[[col_name]] <- col_scale
}
}
row_variables <- do.call(
data.frame,
c(row_variables, list(row.names = rownames(object)))
)
row_annotation_colours <- row_annotation_colours[colnames(row_variables)]
} else {
row_variables <- row_annotation_colours <- NULL
}
if (length(intersect(names(row_annotation_colours), names(column_annotation_colours)))) {
warning("Element with the same name in row and column annotations. ",
"Assuming they're the same.")
}
annotation_colours <- c(row_annotation_colours, column_annotation_colours)
# Creating the heatmap as specified.
pheatmap::pheatmap(
heatmap_scale$x,
color = heatmap_scale$colour,
breaks = heatmap_scale$colour_breaks,
annotation_col = column_variables,
annotation_row = row_variables,
annotation_colors = annotation_colours,
show_colnames = show_colnames,
cluster_cols = cluster_cols,
...
)
}
#' @importFrom ggplot2 scale_colour_gradientn
.heatmap_scale <- function(x, center, scale, colour=NULL, zlim=NULL, symmetric=NULL) {
if (center) {
x <- x - rowMeans(x)
}
if (scale) {
if (!center & any(rowSums(x) == 0)) {
stop("Cannot include non-expressed genes when scale=TRUE.")
}
x <- x / sqrt(rowSums(x^2) / (ncol(x) - 1))
}
if (is.null(zlim)) {
if (center) {
extreme <- max(abs(x))
zlim <- c(-extreme, extreme)
} else {
zlim <- range(x)
}
}
if (is.null(colour)) {
if (center) {
colour <- rev(RColorBrewer::brewer.pal(9, "RdYlBu"))
} else {
colour <- viridis::viridis(9)
}
}
x[x < zlim[1]] <- zlim[1]
x[x > zlim[2]] <- zlim[2]
list(
x = x,
colour = colour,
colour_breaks = seq(zlim[1], zlim[2], length.out=length(colour) + 1L),
colour_scale = scale_colour_gradientn(colours = colour, limits = zlim),
zlim = zlim
)
}
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