setDefault: Set object specific default

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Set object specific default

Description

Sets object specific default for recurring arguments such as pt_alpha, pt_clrp, verbose.

Usage

setDefault(object, ...)

Arguments

object	An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.
...	Named arguments whose default input you want to override.

Value

The updated input object, containing the added, removed or computed results.

Examples

library(SPATA2)

object1 <- loadExampleObject("UKFT269T", meta = TRUE)
object2 <- loadExmapleObject("UKF275T", meta = TRUE)

# current
getDefault(object1, arg = "pt_clrp")
getDefault(object2, arg = "pt_clrp")

# if not specified, the function uses the object specific default
plotSurface(object1, color_by = "bayes_space")
plotSurface(object2, color_by = "bayes_space")

# overwrite
object1 <- setDefault(object1, pt_clrp = "uc")
objct2 <- setDefault(object2, pt_clrp = "jco")

# if not specified, the function uses the object specific default
# default has changed
plotSurface(object1, color_by = "bayes_space")
plotSurface(object2, color_by = "bayes_space")

# manually speciyfing the argument overwrites the default
plotSurface(object1, color_by = "bayes_space", pt_clrp = "jama")
plotSurface(object2, color_by = "bayes_space", pt_clrp = "tab20")

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