plotSurfaceSC.Rd
Plots single cell input on the sample surface.
plotSurfaceSC(
object,
sc_input,
cell_types = NULL,
line_size = 0.5,
pt_alpha = 1,
pt_size = 0.5,
display_density = TRUE,
display_facets = TRUE,
display_image = FALSE,
display_points = TRUE,
clrp = NULL,
clrp_adjust = NULL,
frame_by = "coords",
nrow = NULL,
ncol = NULL
)
An object of class SPATA2
or, in case of S4 generics,
objects of classes for which a method has been defined.
Data.frame that contains the results from single cell deconvolution. Must have at least three columns:
x : numeric. Position of cell on the x axis in pixel.,
y : numeric. Position of cell on the y axis in pixel.,
cell_type : factor Cell type of the cell.
Numeric. Affects size of the main lines of the plot.
Numeric value. Specifies the degree of transparency of all points.
Numeric value. Specifies the size of all points.
Logical value. If TRUE
, uses ggplot2::geom_density2d()
to visualize cell density with contours.
Logical value. If set to TRUE the plot is split via
ggplot2::facet_wrap()
such that each variable gets it's own subplot.
Logical value. If TRUE
, adds the image of the
tissue.
Logical value. If set to TRUE points are used additionally to display the results.
Character value. Specifies the color palette to be used to represent
groups of discrete variables. Run validColorPalettes()
to obtain valid
input options.
Named character vector or NULL. If character, it adjusts the color palette that is used to represent the groups. Names of the input vector must refer to the group and the respective named element denotes the color with which to represent the group.
Numeric values or NULL. Used to arrange multiple plots.
Character value or NULL
. If character,
subsets the cell types that are included in the plots.
Returns a ggplot that can be additionally customized according to the rules of the ggplot2 framework.