plotRowData: Plot row metadata

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

Plot row metadata

Description

Plot row-level (i.e., gene) metadata from a SingleCellExperiment object.

Usage

plotRowData(
  object,
  y,
  x = NULL,
  colour_by = color_by,
  shape_by = NULL,
  size_by = NULL,
  by_exprs_values = "logcounts",
  other_fields = list(),
  color_by = NULL,
  by.assay.type = by_exprs_values,
  ...
)

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 ?retrieveFeatureInfo.
x	String specifying the column-level metadata to show on the x-axis. Alternatively, an AsIs vector or data.frame, see ?retrieveFeatureInfo. If NULL, nothing is shown on the x-axis.
colour_by	Specification of a row metadata field or a cell to colour by, see ?retrieveFeatureInfo for possible values.
shape_by	Specification of a row metadata field or a cell to shape by, see ?retrieveFeatureInfo for possible values.
size_by	Specification of a row metadata field or a cell to size by, see ?retrieveFeatureInfo for possible values.
by_exprs_values	Alias to by.assay.type.
other_fields	Additional feature-based fields to include in the data.frame, see ?"scater-plot-args" for details.
color_by	Alias to colour_by.
by.assay.type	A string or integer scalar specifying which assay to obtain expression values from, for use in point aesthetics - see ?retrieveFeatureInfo for details.
...	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.

Examples

example_sce <- mockSCE()
example_sce <- logNormCounts(example_sce)
rowData(example_sce) <- cbind(rowData(example_sce), 
    perFeatureQCMetrics(example_sce))

plotRowData(example_sce, y="detected", x="mean") +
    scale_x_log10()

Alanocallaghan/scater documentation built on July 18, 2024, 10:58 p.m.