plotOverview: Plot overview of S4 objects

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Plot overview of S4 objects

Description

Assigns every numeric variable to the model it fitted best against and plots the p-value of the fit against the fit evaluation.

Usage

plotOverview(object, ...)

## S4 method for signature 'SpatialAnnotationScreening'
plotOverview(
  object,
  eval = "ias_score",
  pval = "p_value_mean_adjusted",
  pt_alpha = 0.75,
  pt_color = "black",
  pt_size = 1,
  label_vars = NULL,
  label_alpha = 0.9,
  label_color = "black",
  label_size = 2,
  model_subset = NULL,
  nrow = NULL,
  ncol = NULL,
  ...
)

## S4 method for signature 'SpatialTrajectoryScreening'
plotOverview(
  object,
  eval = "sts_score",
  pval = "p_value",
  pt_alpha = 0.75,
  pt_color = "black",
  pt_size = 1,
  label_vars = NULL,
  label_alpha = 0.9,
  label_color = "black",
  label_size = 2,
  model_subset = NULL,
  model_remove = NULL,
  nrow = NULL,
  ncol = NULL,
  ...
)

Arguments

object	An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.
...	Used to absorb deprecated arguments or functions.
eval	Character value. The variable to use for the x-axis.
pval	Character value. The variable to use for the y-axis.
pt_alpha	Numeric value. Specifies the degree of transparency of all points.
pt_size	Numeric value. Specifies the size of all points.
label_vars	Character value, numeric value or NULL. Useful to highlight the exact position/evalation of variables. If character, specifies the variables that are labeled. If numeric, specifies the top n of variables that are labeled. If NULL, ignored.
nrow, ncol	Numeric values or NULL. Used to arrange multiple plots.

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