Add points to base surface plot

Adds a point layer to a base surface plot.

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
)

Arguments

object

An object of class spata2.

color_by

The variable to be displayed by color:

  • Gene set as a single character value. Must be in getGeneSets()

  • Genes as a character vector. If more than one gene is specified the average expression of those genes will be calculated and displayed. Must be in getGenes()

  • Feature as a single character value. Must be in getFeaturenNames()

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

Vector of length two or NULL. If not NULL, specifies the x- and y-range to which the output image is cropped. E.g. xrange = c(200, 500) results in the image being cropped from x-coordinate 200px up to x-coordinate 500px. If NULL, the original image ranges are taken.

This argument works within the SPATA2 distance framework. If values are specified in European units of length the input is immediately converted to pixel units. See info section Distance measures for more information.

Value

Plots right into the plotting window.