ggpLayerGroupOutline | R Documentation |
Highlights groups of barcode-spots by encircling them.
Depending on the plot_type
this can be added to a surface plot
or a dimensional reduction plot.
ggpLayerGroupOutline(
object,
grouping,
groups_subset = NULL,
plot_type = "surface",
line_color = "black",
line_size = 1,
alpha = 0,
bcsp_rm = character(0),
outlier_rm = TRUE,
eps = (getCCD(object, "px") * 1.25),
minPts = 3,
concavity = NULL,
expand_outline = getCCD(object, "px") * 1.1,
...
)
object |
An object of class |
groups_subset |
Character value or NULL. If character, specifies the exact groups that are encircled. If NULL, all groups are encircled. |
plot_type |
Character value. Either 'surface', 'tsne' or 'umap'. |
line_color |
Character. Affects color of the main lines of the plot. |
line_size |
Numeric. Affects size of the main lines of the plot. |
bcsp_rm |
Character vector or |
outlier_rm , minPts |
Logical. If |
concavity |
Given to |
expand_outline |
Distance measure by which the outline of the area is expanded. |
... |
Additional arguments given to |
ggpLayer*()
-functions return lists of ggproto
objects
that can be added to ggplots via the +
operator. In most of the cases
they are supposed to be added to plots created with the plotSurface*()
family.
object <- downloadPubExample("269_T")
plotImageGgplot(object) +
ggpLayerGroupOutline(
object = object,
plot_type = "surface",
grouping = "histology",
groups_subset = "tumor",
line_color = color_vector("npg")[1]
)
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