renameGroups: Rename cluster/group names

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Rename cluster/group names

Description

Allows to rename groups within a grouping variable. Make sure to rename tissue sections with renameTissueSection()!

Usage

renameGroups(object, grouping, ..., keep_levels = NULL)

renameTissueSection(object, ...)

Arguments

object	An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.
grouping	Character value. The grouping variable of interest. Use getGroupingOptions() to obtain all valid input options.
...	The groups to be renamed specified according to the following syntax: 'new_group_name' = 'old_group_name'.

See Also

relevelGroups()

Examples

library(SPATA2)

data("example_data")

## Example 1 - rename normal grouping variables

object <- example_data$object_UKF269T_diet

plotSurface(object, color_by = "histology")

object <-
 renameGroups(
  object = object,
  grouping = "histology",
  "hist1" = "tumor", "hist2" = "transition", "hist3" = "infiltrated"
  )

plotSurface(object, color_by = "histology")

## Example 2 - rename tissue secions

object <- example_data$object_lmu_mci_diet

object <- identifyTissueOutline(object)

plotSurface(object, color_by = "tissue_section")

object <-
 renameTissueSection(
   object = object,
   "lower_hemisphere" = "tissue_section_1", "upper_hemisphere" = "tissue_section_2"
   )

plotSurface(object, color_by = "tissue_section")

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