plotColData: Plot column metadata

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

Description

Plot column-level (i.e., cell) metadata in an SingleCellExperiment object.

Usage

plotColData(
  object,
  y,
  x = NULL,
  colour_by = NULL,
  shape_by = NULL,
  size_by = NULL,
  by_exprs_values = "logcounts",
  other_fields = list(),
  swap_rownames = NULL,
  ...
)

Arguments

object	A SingleCellExperiment object containing expression values and experimental information.
y	String specifying the column-level metadata field to show on the y-axis. Alternatively, an AsIs vector or data.frame, see ?retrieveCellInfo.
x	String specifying the column-level metadata to show on the x-axis. Alternatively, an AsIs vector or data.frame, see ?retrieveCellInfo. If NULL, nothing is shown on the x-axis.
colour_by	Specification of a column metadata field or a feature to colour by, see the by argument in ?retrieveCellInfo for possible values.
shape_by	Specification of a column metadata field or a feature to shape by, see the by argument in ?retrieveCellInfo for possible values.
size_by	Specification of a column metadata field or a feature to size by, see the by argument in ?retrieveCellInfo for possible values.
by_exprs_values	A string or integer scalar specifying which assay to obtain expression values from, for use in point aesthetics - see ?retrieveCellInfo for details.
other_fields	Additional cell-based fields to include in the data.frame, see ?"scater-plot-args" for details.
swap_rownames	Column name of rowData(object) to be used to identify features instead of rownames(object) when labelling plot elements.
...	Additional arguments for visualization, see ?"scater-plot-args" for details.

Details

If y is continuous and x=NULL, a violin plot is generated. If x is categorical, a grouped violin plot will be generated, with one violin for each level of x. If x is continuous, a scatter plot will be generated.

If y is categorical and x is continuous, horizontal violin plots will be generated. If x is missing or categorical, rectangule plots will be generated where the area of a rectangle is proportional to the number of points for a combination of factors.

Value

A ggplot object.

Author(s)

Davis McCarthy, with modifications by Aaron Lun

Examples

example_sce <- mockSCE()
example_sce <- logNormCounts(example_sce)
colData(example_sce) <- cbind(colData(example_sce), 
    perCellQCMetrics(example_sce))

plotColData(example_sce, y = "detected", x = "sum", 
   colour_by = "Mutation_Status") + scale_x_log10()

plotColData(example_sce, y = "detected", x = "sum", 
   colour_by = "Mutation_Status", size_by = "Gene_0001", 
   shape_by = "Treatment") + scale_x_log10()

plotColData(example_sce, y = "Treatment", x = "sum", 
   colour_by = "Mutation_Status") + scale_y_log10() # flipped violin.

plotColData(example_sce, y = "detected", 
   x = "Cell_Cycle", colour_by = "Mutation_Status")

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