plotReducedDim {scater} | R Documentation |
Plot cell-level reduced dimension results stored in a SingleCellExperiment object.
plotReducedDim( object, dimred, ncomponents = 2, percentVar = NULL, colour_by = NULL, shape_by = NULL, size_by = NULL, by_exprs_values = "logcounts", text_by = NULL, text_size = 5, text_colour = "black", label_format = c("%s %i", " (%i%%)"), other_fields = list(), swap_rownames = NULL, ... )
object |
A SingleCellExperiment object. |
dimred |
A string or integer scalar indicating the reduced dimension
result in |
ncomponents |
A numeric scalar indicating the number of dimensions to plot, starting from the first dimension. Alternatively, a numeric vector specifying the dimensions to be plotted. |
percentVar |
A numeric vector giving the proportion of variance in
expression explained by each reduced dimension.
Only expected to be used in PCA settings, e.g., in the
|
colour_by |
Specification of a column metadata field or a feature to
colour by, see the |
shape_by |
Specification of a column metadata field or a feature to
shape by, see the |
size_by |
Specification of a column metadata field or a feature to
size by, see the |
by_exprs_values |
A string or integer scalar specifying which assay to
obtain expression values from,
for use in point aesthetics - see the |
text_by |
String specifying the column metadata field with which to add
text labels on the plot.
This must refer to a categorical field, i.e., coercible into a factor.
Alternatively, an AsIs vector or data.frame, see
|
text_size |
Numeric scalar specifying the size of added text. |
text_colour |
String specifying the colour of the added text. |
label_format |
Character vector of length 2 containing format strings
to use for the axis labels.
The first string expects a string containing the result type (e.g.,
|
other_fields |
Additional cell-based fields to include in the
data.frame, see |
swap_rownames |
Column name of |
... |
Additional arguments for visualization, see
|
If ncomponents
is a scalar equal to 2, a scatterplot of the first two
dimensions is produced.
If ncomponents
is greater than 2, a pairs plots for the top
dimensions is produced.
Alternatively, if ncomponents
is a vector of length 2, a scatterplot
of the two specified dimensions is produced.
If it is of length greater than 2, a pairs plot is produced containing all
pairwise plots between the specified dimensions.
The text_by
option will add factor levels as labels onto the plot,
placed at the median coordinate across all points in that level.
This is useful for annotating position-related metadata (e.g., clusters)
when there are too many levels to distinguish by colour.
It is only available for scatterplots.
A ggplot object
Davis McCarthy, with modifications by Aaron Lun
example_sce <- mockSCE() example_sce <- logNormCounts(example_sce) example_sce <- runPCA(example_sce, ncomponents=5) plotReducedDim(example_sce, "PCA") plotReducedDim(example_sce, "PCA", colour_by="Cell_Cycle") plotReducedDim(example_sce, "PCA", colour_by="Gene_0001") plotReducedDim(example_sce, "PCA", ncomponents=5) plotReducedDim(example_sce, "PCA", ncomponents=5, colour_by="Cell_Cycle", shape_by="Treatment")