plotRowData {scater} | R Documentation |
Plot row-level (i.e., gene) metadata from a SingleCellExperiment object.
plotRowData( object, y, x = NULL, colour_by = NULL, shape_by = NULL, size_by = NULL, by_exprs_values = "logcounts", other_fields = list(), ... )
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 |
x |
String specifying the column-level metadata to show on the x-axis.
Alternatively, an AsIs vector or data.frame, see |
colour_by |
Specification of a row metadata field or a cell to colour by, see |
shape_by |
Specification of a row metadata field or a cell to shape by, see |
size_by |
Specification of a row metadata field or a cell to size by, see |
by_exprs_values |
A string or integer scalar specifying which assay to obtain expression values from,
for use in point aesthetics - see |
other_fields |
Additional feature-based fields to include in the data.frame, see |
... |
Additional arguments for visualization, see |
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.
A ggplot object.
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()