plotSurfaceAverage: Plot several surface plots colored by gene averages

In kueckelj/SPATA2: A Toolbox for Spatial Gene Expression Analysis

Plot several surface plots colored by gene averages

Description

Displays the spatial dimension of the sample and colors the surface according to the expression of averaged gene expression values. For each element in the list specified in argument color_by a surface plot is generated colored by the gene's average expression score.

Usage

plotSurfaceAverage(
  object,
  color_by,
  pt_alpha = NULL,
  pt_clrsp = NULL,
  pt_size = NULL,
  smooth = FALSE,
  smooth_span = NULL,
  use_scattermore = FALSE,
  sctm_pixels = c(1024, 1024),
  sctm_interpolate = FALSE,
  display_image = NULL,
  bcsp_rm = NULL,
  na_rm = FALSE,
  ...
)

Arguments

object	An object of class spata2.
color_by	A character vector of gene names or a named list in which each element is a vector of gene names.
pt_alpha	Numeric value. Specifies the degree of transparency of all points.
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.
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().
use_scattermore	Logical value. If TRUE, data points are plotted with scattermore::geom_scattermore() which allows quick plotting of several thousand data points. If the number of data points plotted is bigger than 10.000 it is used anyway.
sctm_interpolate, sctm_pixels	Given to the corresponding arguments of scattermore::geom_scattermore(). Note: With increasing sctm_pixels the point size must be adjusted with the argument pt_size.
display_image	Logical. If set to TRUE the histology image of the specified sample is displayed underneath the plot.
bcsp_rm	Character vector or NULL. If character, specifies barcode-spots that are removed before analysis or plotting.
...	Used to absorb deprecated arguments or functions.

Examples

#Not run:

color_by_list <- list(Example1 = c("PGK1", "PDK1", "GBE1"),
                      Example2 = c("METRN", "GFAP")
                      )

plotSurfaceAverage(
   object = spata_obj,
   color_by = color_by_list
 )

kueckelj/SPATA2 documentation built on March 16, 2024, 10:25 a.m.