Plot scaled vs. denoised expression — plotAutoencoderResults • SPATA2

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

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.
of_sample: This argument is currently inactive. It might be reactivated when spata-objects can store more than one sample.

Value

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

Details

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