plotAutoencoderResults: Plot scaled vs. denoised expression

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Plot scaled vs. denoised expression

Description

Compares the distribution of the expression levels of genes between the scaled matrix and the denoised matrix.

Usage

plotAutoencoderResults(
  object,
  genes,
  mtr_name = "denoised",
  normalize = NULL,
  scales = NULL,
  pt_alpha = NULL,
  pt_clrp = NULL,
  pt_size = NULL,
  verbose = NULL,
  of_sample = NA,
  ...
)

Arguments

object	A valid spata-object.
genes	Character vector of length two. Denotes the genes to be used for the validation plot.
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_size	Numeric value. Specifies the size of all points.
verbose	Logical. If TRUE, informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)
of_sample	This argument is currently inactive. It might be reactivated when spata-objects can store more than one sample.

Details

This function requires a denoised matrix in slot @data generated by runAutoEncoderDenoising() as well as a scaled matrix.

Value

Returns a ggplot that can be additionally customized according to the rules of the ggplot2 framework.

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