plotRowData {scater}R Documentation

Plot row metadata

Description

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

Usage

plotRowData(object, y, x = NULL, colour_by = NULL, shape_by = NULL,
  size_by = NULL, by_exprs_values = "logcounts",
  by_show_single = FALSE, ...)

plotFeatureData(...)

Arguments

object

A SingleCellExperiment object containing expression values and experimental information.

y

Specification of the row-level metadata to show on the y-axis, see ?"scater-vis-var" for possible values. Note that only metadata fields will be searched, assays will not be used.

x

Specification of the row-level metadata to show on the x-axis, see ?"scater-vis-var" for possible values. Again, only metadata fields will be searched, assays will not be used.

colour_by

Specification of a row metadata field or a cell to colour by, see ?"scater-vis-var" for possible values.

shape_by

Specification of a row metadata field or a cell to shape by, see ?"scater-vis-var" for possible values.

size_by

Specification of a row metadata field or a cell to size by, see ?"scater-vis-var" 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 ?"scater-vis-var" for details.

by_show_single

Logical scalar specifying whether single-level factors should be used for point aesthetics, see ?"scater-vis-var" 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.

Note that plotFeatureData is a synonym for plotRowData. This is an artifact of the transition from the old SCESet class, and will be deprecated in future releases.

Value

A ggplot object.

Examples

data("sc_example_counts")
data("sc_example_cell_info")
example_sce <- SingleCellExperiment(
    assays = list(counts = sc_example_counts), 
    colData = sc_example_cell_info
)
example_sce <- calculateQCMetrics(example_sce,
    feature_controls = list(ERCC=1:40))
example_sce <- normalize(example_sce)

plotRowData(example_sce, y="n_cells_by_counts", x="log10_total_counts")
plotRowData(example_sce, y="n_cells_by_counts", 
   size_by ="log10_total_counts",
   colour_by = "is_feature_control")
[Package scater version 1.10.1 Index]