plotSurfaceIAS | R Documentation |
Plots the surface of the sample three times with different
coloring to visualize how imageAnnotationScreening()
screens
the sample depending on the input of arguments binwidth
, n_bins_circle
,
n_bins_angle
.
plotSurfaceIAS(object, ...)
## S4 method for signature 'spata2'
plotSurfaceIAS(
object,
id,
distance = NA_integer_,
binwidth = getCCD(object),
n_bins_circle = NA_integer_,
angle_span = c(0, 360),
n_bins_angle = 1,
outer = TRUE,
inner = TRUE,
pt_alpha = NA_integer_,
pt_clrp = c("inferno", "default"),
pt_clrsp = "inferno",
pt_size = NULL,
color_core = ggplot2::alpha("grey", 0),
color_outside = ggplot2::alpha("lightgrey", 0.25),
show_plots = TRUE,
display_angle = FALSE,
display_bins_angle = TRUE,
display_bins_circle = TRUE,
ggpLayers = list(),
remove_circle_bins = FALSE,
bcsp_exclude = NULL,
verbose = NULL,
...
)
## S4 method for signature 'ImageAnnotationScreening'
plotSurfaceIAS(
object,
pt_alpha = NA_integer_,
pt_clrp = c("inferno", "default"),
pt_clrsp = "inferno",
pt_size = 2.25,
color_core = ggplot2::alpha("grey", 0),
color_outside = ggplot2::alpha("lightgrey", 0.25),
show_plots = TRUE,
display_angle = FALSE,
display_bins_angle = TRUE,
display_bins_circle = TRUE,
ggpLayers = list(),
...
)
object |
An object of class |
... |
Used to absorb deprecated arguments or functions. |
id |
Character value. The ID of the image annotation of interest. |
distance |
Distance value. Specifies the distance from the border of the
image annotation to the horizon in the periphery up to which the screening
is conducted. (See details for more.) - See details of |
binwidth |
Distance value. The width of the circular bins to which
the barcode-spots are assigned. We recommend to set it equal to the center-center
distance: |
n_bins_circle |
Numeric value or vector of length 2. Specifies how many times the area is buffered with the value
denoted in |
angle_span |
Numeric vector of length 2. Confines the area screened by an angle span relative to the center of the image annotation. (See details fore more.) |
n_bins_angle |
Numeric value. Number of bins that are created by angle. (See details for more.) |
outer |
Logical value. Only applies if an image annotation contains a secondary image annotation within its own area. If |
inner |
Logical value. Only applies if an image annotation contains a secondary image annotation within its own area. If |
pt_alpha |
Numeric value. Specifies the degree of transparency of all points. |
pt_clrp |
The color palette to be used if the specified variable displayed by
color is categorical/discrete. Run |
pt_clrsp |
The color spectrum to be used if the specified variable displayed by
color is continuous. Run |
pt_size |
Numeric value. Specifies the size of all points. |
color_core , color_outside |
Character value. Denotes
the colors with which the area of image annotation ( |
show_plots |
Logical value. If TRUE, the plots are immediately plotted. If FALSE, only a list of plots is returned (invisibly). |
display_angle , display_bins_angle , display_circle |
Logical value. If TRUE, the plot is included. If FALSE, plotting is skipped. |
ggpLayers |
List of |
bcsp_exclude |
Character value containing name(s) of barcode-spots to be excluded from the analysis. |
verbose |
Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.) |
The method for class ImageAnnotationScreening
(the output of
the function imageAnnotationScreening()
) can be used
to show the area on which the results base. Therefore, it does not have
arguments binwidth
, n_bins_circle
and n_bins_angle
.
An invisible list of ggplots.
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