ggsce: Create a ggplot from a SingleCellExperiment

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

Create a ggplot from a SingleCellExperiment

Description

Create a base ggplot object from a SingleCellExperiment, the contents of which can be directly referenced in subsequent layers without prior specification.

Usage

ggcells(
  x,
  mapping = aes(),
  features = NULL,
  exprs_values = "logcounts",
  use_dimred = TRUE,
  use_altexps = FALSE,
  prefix_altexps = FALSE,
  check_names = TRUE,
  extract_mapping = TRUE,
  assay.type = exprs_values,
  ...
)

ggfeatures(
  x,
  mapping = aes(),
  cells = NULL,
  exprs_values = "logcounts",
  check_names = TRUE,
  extract_mapping = TRUE,
  assay.type = exprs_values,
  ...
)

Arguments

x	A SingleCellExperiment object. This is expected to have row names for ggcells and column names for ggfeatures.
mapping	A list containing aesthetic mappings, usually the output of aes or related functions.
features	Character vector specifying the features for which to extract expression profiles across cells. May also include features in alternative Experiments if permitted by use.altexps.
exprs_values, use_dimred, use_altexps, prefix_altexps, check_names	Soft-deprecated equivalents of the arguments described above.
extract_mapping	Logical scalar indicating whether features or cells should be automatically expanded to include variables referenced in mapping.
assay.type	String or integer scalar specifying the expression values for which to compute the variance (also an alias exprs_value is accepted).
...	Further arguments to pass to ggplot.
cells	Character vector specifying the features for which to extract expression profiles across cells.

Details

These functions generate a data.frame from the contents of a SingleCellExperiment and pass it to ggplot. Rows, columns or metadata fields in the x can then be referenced in subsequent ggplot2 commands.

ggcells treats cells as the data values so users can reference row names of x (if provided in features), column metadata variables and dimensionality reduction results. They can also reference row names and metadata variables for alternative Experiments.

ggfeatures treats features as the data values so users can reference column names of x (if provided in cells) and row metadata variables.

If mapping is supplied, the function will automatically expand features or cells for any features or cells requested in the mapping. This is convenient as features/cells do not have to specified twice (once in data.frame construction and again in later geom or stat layers). Developers may wish to turn this off with extract_mapping=FALSE for greater control.

Value

A ggplot object containing the specified contents of x.

Author(s)

Aaron Lun

See Also

makePerCellDF and makePerFeatureDF, for the construction of the data.frame.

Examples

example_sce <- mockSCE()
example_sce <- logNormCounts(example_sce)
example_sce <- runPCA(example_sce)

ggcells(example_sce, aes(x=PCA.1, y=PCA.2, colour=Gene_0001)) +
    geom_point()

ggcells(example_sce, aes(x=Mutation_Status, y=Gene_0001)) +
    geom_violin() +
    facet_wrap(~Cell_Cycle)

rowData(example_sce)$GC <- runif(nrow(example_sce))
ggfeatures(example_sce, aes(x=GC, y=Cell_001)) +
    geom_point() +
    stat_smooth()

Alanocallaghan/scater documentation built on Feb. 10, 2024, 6:28 a.m.