Base plotting function for all Spatial plots
SingleSpatialPlot(
data,
image,
cols = NULL,
image.alpha = 1,
pt.alpha = NULL,
crop = TRUE,
pt.size.factor = NULL,
stroke = 0.25,
col.by = NULL,
alpha.by = NULL,
cells.highlight = NULL,
cols.highlight = c("#DE2D26", "grey50"),
geom = c("spatial", "interactive", "poly"),
na.value = "grey50"
)
A ggplot2 object
Data.frame with info to be plotted
SpatialImage
object to be plotted
Vector of colors, each color corresponds to an identity class.
This may also be a single character
or numeric value corresponding to a palette as specified by
brewer.pal.info
. By default, ggplot2 assigns
colors
Adjust the opacity of the background images. Set to 0 to remove.
Adjust the opacity of the points if plotting a
SpatialDimPlot
Crop the plot in to focus on points plotted. Set to FALSE
to show entire background image.
Sets the size of the points relative to spot.radius
Control the width of the border around the spots
Mapping variable for the point color
Mapping variable for the point alpha value
A list of character or numeric vectors of cells to highlight. If only one group of cells desired, can simply pass a vector instead of a list. If set, colors selected cells to the color(s) in cols.highlight
A vector of colors to highlight the cells as; ordered the same as the groups in cells.highlight; last color corresponds to unselected cells.
Switch between normal spatial geom and geom to enable hover functionality
Color for spots with NA values