plotHeatmap {scater}R Documentation

Plot heatmap of gene expression values

Description

Create a heatmap of expression values for each cell and specified features in a SingleCellExperiment object.

Usage

plotHeatmap(object, features, columns = NULL, exprs_values = "logcounts",
  center = FALSE, zlim = NULL, symmetric = FALSE, color = NULL,
  colour_columns_by = NULL, by_exprs_values = exprs_values,
  by_show_single = FALSE, ...)

Arguments

object

A SingleCellExperiment object.

features

A character vector of row names, a logical vector of integer vector of indices specifying rows of object to show in the heatmap.

columns

A vector specifying the subset of columns in object to show as columns in the heatmp. By default, all columns are used in their original order.

exprs_values

A string or integer scalar indicating which assay of object should be used as expression values for colouring in the heatmap.

center

A logical scalar indicating whether each row should have its mean expression centered at zero prior to plotting.

zlim

A numeric vector of length 2, specifying the upper and lower bounds for the expression values. This winsorizes the expression matrix prior to plotting (but after centering, if center=TRUE). If NULL, it defaults to the range of the expression matrix.

symmetric

A logical scalar specifying whether the default zlim should be symmetric around zero. If TRUE, the maximum absolute value of zlim will be computed and multiplied by c(-1, 1) to redefine zlim.

color

A vector of colours specifying the palette to use for mapping expression values to colours. This defaults to the default setting in pheatmap.

colour_columns_by

A list of values specifying how the columns should be annotated with colours. Each entry of the list can be of the form described by ?"scater-vis-var". A character vector can also be supplied and will be treated as a list of strings.

by_exprs_values

A string or integer scalar specifying which assay to obtain expression values from, for colouring of column-level data - see ?"scater-vis-var" for details.

by_show_single

Logical scalar specifying whether single-level factors should be used for column-level colouring, see ?"scater-vis-var" for details.

...

Additional arguments to pass to pheatmap.

Details

Setting 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 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

Examples

example(normalizeSCE) # borrowing the example objects in here.
plotHeatmap(example_sce, features=rownames(example_sce)[1:10])
plotHeatmap(example_sce, features=rownames(example_sce)[1:10],
    center=TRUE, symmetric=TRUE)

plotHeatmap(example_sce, features=rownames(example_sce)[1:10],
    colour_columns_by=c("Mutation_Status", "Cell_Cycle"))


[Package scater version 1.8.4 Index]