plotSurfaceQuantiles | R Documentation |
This function calculates the quantiles specified in n_qntl
of the numeric variable specified in color_by
and divides the barcode
spots accordingly. If you want to grey-out certain quantiles use argument keep_qntls
.
plotSurfaceQuantiles(
object,
color_by,
alpha_by = NULL,
n_qntls = 5,
keep_qntls = 1:n_qntls,
pt_alpha = NULL,
pt_clrp = NULL,
pt_size = NULL,
smooth = NULL,
smooth_span = NULL,
display_image = NULL,
bcsp_rm = NULL,
use_scattermore = FALSE,
sctm_pixels = c(1024, 1024),
sctm_interpolate = FALSE,
verbose = NULL,
...
)
object |
An object of class |
color_by |
Character value. Specifies the numeric variable of interest:
|
n_qntls |
Numeric value. Specifies the number of bins in which to distribute the barcode spots. |
keep_qntls |
Numeric vector. Specifies the quantiles to highlight by color. The remaining ones are displayed in grey. |
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_size |
Numeric value. Specifies the size of all points. |
smooth |
Logical. If TRUE, a loess fit is used to smooth the values. |
smooth_span |
Numeric value. Controls the degree of smoothing.
Given to argument |
display_image |
Logical. If set to TRUE the histology image of the specified sample is displayed underneath the plot. |
bcsp_rm |
Character vector or |
use_scattermore |
Logical value. If |
sctm_interpolate , sctm_pixels |
Given to the corresponding arguments
of |
verbose |
Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.) |
... |
Used to absorb deprecated arguments or functions. |
A ggplot.
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