plotHeatmap: Plot heatmap of gene expression values

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

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,
  column_annotation_colors = list(),
  order_columns_by = NULL,
  by_exprs_values = exprs_values,
  show_colnames = FALSE,
  cluster_cols = is.null(order_columns_by),
  swap_rownames = NULL,
  ...
)

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 heatmap. Also specifies the column order if cluster_cols=FALSE and order_columns_by=NULL. By default, all columns are used.
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 any acceptable input to the by argument in ?retrieveCellInfo. A character vector can also be supplied and will be treated as a list of strings.
column_annotation_colors	A named list of color scales to be used for the column annotations specified in colour_columns_by. Names should be character values present in colour_columns_by, If a color scale is not specified for a particular annotation, a default color scale is chosen. The full list of colour maps is passed to pheatmap as the annotation_colours argument.
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 by argument in ?retrieveCellInfo. A character vector can also be supplied and will be treated as a list of strings. This argument is automatically appended to colour_columns_by.
by_exprs_values	A string or integer scalar specifying which assay to obtain expression values from, for colouring of column-level data - see the exprs_values argument in ?retrieveCellInfo.
show_colnames, cluster_cols, ...	Additional arguments to pass to pheatmap.
swap_rownames	Column name of rowData(object) to be used to identify features instead of rownames(object) when labelling plot elements.

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.

Setting order_columns_by is useful for automatically ordering the heatmap by one or more factors of interest, e.g., cluster identity. This the need to set colour_columns_by, cluster_cols and columns to achieve the same effect.

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_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, symmetric=TRUE)

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

scater documentation built on Feb. 28, 2021, 2:01 a.m.