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Quantile heatmap

Source: R/AllGenerics.R, R/plotQuantileHeatmap-methods.R
plotQuantileHeatmap.Rd

Quantile heatmap

Usage

plotQuantileHeatmap(object, ...)

# S4 method for SingleCellExperiment
plotQuantileHeatmap(object, ...)

# S4 method for SummarizedExperiment
plotQuantileHeatmap(
  object,
  assay = 1L,
  interestingGroups = NULL,
  n = 10L,
  clusterRows = TRUE,
  clusterCols = TRUE,
  showRownames = isTRUE(nrow(object) <= 30L),
  showColnames = TRUE,
  treeheightRow = 50L,
  treeheightCol = 50L,
  color = getOption(x = "acid.heatmap.quantile.color", default = viridis::magma),
  legendColor = getOption(x = "acid.heatmap.legend.color", default =
    AcidPlots::synesthesia),
  legend = FALSE,
  borderColor = NULL,
  title = NULL,
  convertGenesToSymbols = showRownames,
  ...
)

Arguments

object

Object.

...

Additional arguments.

assay

vector(1). Assay name or index position.

interestingGroups

character. Groups of interest to use for visualization. Corresponds to factors describing the columns of the object.

n

integer(1). The number of quantile breaks to create.

clusterRows, clusterCols

logical(1). Arrange with hierarchical clustering.

showRownames, showColnames

logical(1). Show row or column names.

treeheightRow, treeheightCol

integer(1). Size of the row and column dendrograms. Use 0 to disable.

color

function, character, or NULL. Hexadecimal color function or values to use for plot.

We generally recommend these hexadecimal functions from the viridis package, in addition to our synesthesia() palette:

Alternatively, colors can be defined manually using hexadecimal values (e.g. c("#FF0000", "#0000FF")), but this is not generally recommended. Refer to the RColorBrewer package for hexadecimal color palettes that may be suitable. If set NULL, will use the default pheatmap colors.

legendColor

function or NULL. Hexadecimal color function to use for legend labels. Note that hexadecimal values are not supported. If set NULL, will use the default pheatmap colors.

legend

logical(1). Show the color legend.

borderColor

character(1) or NULL. Border color.

title

character(1). Title.

convertGenesToSymbols

logical(1). Attempt to automatically convert gene identifiers to gene symbols. Only applies when object contains mappings defined in rowRanges.

Value

Plot.

Note

Updated 2022-03-07.

Examples

data(
    RangedSummarizedExperiment,
    SingleCellExperiment_splatter,
    package = "AcidTest"
)

## SummarizedExperiment ====
object <- RangedSummarizedExperiment
plotQuantileHeatmap(object)


## SingleCellExperiment ====
object <- SingleCellExperiment_splatter
plotQuantileHeatmap(object)