plotHeatmap: Plot heatmap of gene expression values

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

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,
  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,
  ...
)

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.
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	Alias to assay.type.
center	A logical scalar indicating whether each feature should have its mean expression centered at zero prior to plotting.
scale	A logical scalar specifying whether each feature should have its expression values scaled to have 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.
color, color_columns_by, column_annotation_colors, color_rows_by, row_annotation_colors	Aliases to color, color_columns_by, column_annotation_colors, color_rows_by, row_annotation_colors.
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_colours	A named list of colour 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 colour scale is not specified for a particular annotation, a default colour scale is chosen. The full list of colour maps is passed to pheatmap as the annotation_colours argument.
row_annotation_colours	Similar to column_annotation_colours but relating to row annotation rather than column annotation.
colour_rows_by	Similar to colour_columns_by but for rows rather than columns. Each entry of the list can be any acceptable input to the by argument in ?retrieveFeatureInfo.
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	Alias to by.assay.type.
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.
assay.type	A string or integer scalar indicating which assay of object should be used as expression values.
by.assay.type	A string or integer scalar specifying which assay to obtain expression values from, for colouring of column-level data - see the assay.type argument in ?retrieveCellInfo.

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 avoids 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)

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

davismcc/scater documentation built on Feb. 10, 2024, 10:53 a.m.