addPointsBase: Add points to base surface plot

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Add points to base surface plot

Description

Adds a point layer to a base surface plot.

Usage

addPointsBase(
  object,
  color_by,
  alpha_by = NULL,
  pt_alpha = 0.75,
  pt_size = 1,
  pt_clrp = "default",
  pt_clrsp = "inferno",
  clrp_adjust = NULL,
  smooth = NULL,
  smooth_span = NULL,
  xrange = NULL,
  yrange = NULL,
  scale_fct = 1
)

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_size	Numeric value. Specifies the size 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.
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.

Value

Plots right into the plotting window.

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