plotSurfaceBase.Rd
Uses Rs base plotting device instead of ggplot2. This is usually faster but can not make use of the mechanism ggplot2 offers.
plotSurfaceBase(
object,
color_by = NULL,
alpha_by = NULL,
pt_alpha = 0.9,
pt_color = "grey",
pt_clrp = "milo",
pt_clrsp = "inferno",
pt_size = 1,
clrp_adjust = NULL,
smooth = FALSE,
smooth_span = 0.2,
display_axes = FALSE,
display_axes_title = FALSE,
display_image = NULL,
highlight_barcodes = NULL,
highlight_alpha = 0.75,
highlight_color = "orange",
xrange = NULL,
yrange = NULL,
adjust_pt_size = TRUE,
expand = 0,
pty = "s",
verbose = NULL,
unit = "px",
...
)
An object of class SPATA2
or, in case of S4 generics,
objects of classes for which a method has been defined.
Character value. The variables by which to color the data points.
Numeric value. Specifies the degree of transparency of all points.
The color palette to be used if the specified variable displayed by
color is categorical/discrete. Run validColorPalettes()
to see valid input.
The color spectrum to be used if the specified variable displayed by
color is continuous. Run validColorSpectra()
to see valid input.
Numeric value. Specifies the size of all points.
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.
Logical. If TRUE, a loess fit is used to smooth the values.
Numeric value. Controls the degree of smoothing.
Given to argument span
of stats::loess()
.
Distance vector of length
two or NULL
. If not NULL
, specifies the x- and y-range to which
the spatial output is cropped. E.g. xrange = c(200, 500)
results in
the two dimensional space being cropped from x-coordinate 200px up to
x-coordinate 500px. If NULL
, the original range is used.
Specifies image expansion. An image that is cropped based on an image
annotation centers around the image annotation. If expand = 0
, the default, the dimensions of the image,
that is width/x-axis and height/y-axis, are set to include only the image annotation area
and nothing more. Using expand
, the cropped image section can be adjusted. See section
Expansion of cropped image sections for more information.
Logical. If TRUE
, informative messages regarding
the computational progress will be printed.
(Warning messages will always be printed.)
Character value. Specifies the desired unit in
which distance measures
or area measures are provided.
Run validUnitsOfLength()
or validUnitsOfArea()
for valid
input options.
Used to absorb deprecated arguments or functions.
Plots right into the plotting window.