plotSurfaceBase: Plot surface with R base plotting

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Plot surface with R base plotting

Description

Uses Rs base plotting device instead of ggplot2. This is usually faster but can not make use of the mechanism ggplot2 offers.

Usage

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",
  ...
)

Arguments

object	An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.
color_by	Character value. The variables by which to color the data points.
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 validColorPalettes() to see valid input.
pt_clrsp	The color spectrum to be used if the specified variable displayed by color is continuous. Run validColorSpectra() to see valid input.
pt_size	Numeric value. Specifies the size of all points.
clrp_adjust	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.
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 span of stats::loess().
xrange, yrange	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.
expand	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.
verbose	Logical. If TRUE, informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)
unit	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.

Value

Plots right into the plotting window.

theMILOlab/SPATA2 documentation built on Feb. 8, 2025, 11:41 p.m.