plotGroupedHeatmap: Plot heatmap of group-level expression averages

In Alanocallaghan/scater: Single-Cell Analysis Toolkit for Gene Expression Data in R

Plot heatmap of group-level expression averages

Description

Create a heatmap of average expression values for each group of cells and specified features in a SingleCellExperiment object.

Usage

plotGroupedHeatmap(
  object,
  features,
  group,
  block = NULL,
  columns = NULL,
  exprs_values = "logcounts",
  center = FALSE,
  scale = FALSE,
  zlim = NULL,
  colour = color,
  swap_rownames = NULL,
  color = NULL,
  assay.type = exprs_values,
  ...
)

Arguments

object	A SingleCellExperiment object.
features	A character (or factor) vector of row names, a logical vector, or integer vector of indices specifying rows of 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.
group	String specifying the field of colData(object) containing the grouping factor, e.g., cell types or clusters. Alternatively, any value that can be used in the by argument to retrieveCellInfo.
block	String specifying the field of colData(object) containing a blocking factor (e.g., batch of origin). Alternatively, any value that can be used in the by argument to retrieveCellInfo.
columns	A vector specifying the subset of columns in object to use when computing averages.
exprs_values	Alias to assay.type.
center	A logical scalar indicating whether each feature should have its mean expression (specifically, the mean of averages across all groups) centered at zero prior to plotting.
scale	A logical scalar specifying whether each row should have its average expression values scaled to unit variance prior to plotting.
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 NULL, it defaults to the range of the expression matrix. If center=TRUE, this defaults to the range of the centered expression matrix, made symmetric around zero.
colour	A vector of colours specifying the palette to use for increasing expression. This defaults to viridis if center=FALSE, and the the "RdYlBu" colour palette from brewer.pal otherwise.
swap_rownames	Column name of rowData(object) to be used to identify features instead of rownames(object) when labelling plot elements.
color	Alias to colour.
assay.type	A string or integer scalar indicating which assay of object should be used as expression values.
...	Additional arguments to pass to pheatmap.

Details

This function shows the average expression values for each group of cells on a heatmap, as defined using the group factor. A per-group visualization can be preferable to a per-cell visualization when dealing with large number of cells or groups with different size. If block is also specified, the block effect is regressed out of the averages with correctGroupSummary prior to visualization.

Setting center=TRUE is useful for examining log-fold changes of each group's expression profile from the average across all groups. This avoids issues with the entire row appearing a certain colour because the gene is highly/lowly expressed across all cells.

Setting zlim preserves the dynamic range of colours in the presence of outliers. Otherwise, the plot may be dominated by a few genes, which will “flatten” the observed colours for the rest of the heatmap.

Value

A heatmap is produced on the current graphics device. The output of pheatmap is invisibly returned.

Author(s)

Aaron Lun

See Also

pheatmap, for the underlying function.

plotHeatmap, for a per-cell heatmap.

Examples

example_sce <- mockSCE()
example_sce <- logNormCounts(example_sce)
example_sce$Group <- paste0(example_sce$Treatment, "+", example_sce$Mutation_Status)

plotGroupedHeatmap(example_sce, features=rownames(example_sce)[1:10],
    group="Group")

plotGroupedHeatmap(example_sce, features=rownames(example_sce)[1:10],
    group="Group", center=TRUE)

plotGroupedHeatmap(example_sce, features=rownames(example_sce)[1:10],
    group="Group", block="Cell_Cycle", center=TRUE)

Alanocallaghan/scater documentation built on July 18, 2024, 10:58 p.m.