addProcessedMatrix: Add a processed matrix

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Add a processed matrix

Description

Adds a processed matrix to the chosen molecular assay of the object.

Usage

addProcessedMatrix(
  object,
  proc_mtr,
  mtr_name,
  assay_name = activeAssay(object),
  overwrite = FALSE,
  ...
)

Arguments

object	An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.
mtr_name	A character value that denotes the name of the matrix with which one can refer to it in subsequent functions via mtr_name.
assay_name	Only relevant if the SPATA2 object contains more than one assay: Denotes the assay of interest and thus the molecular modality to use. Defaults to the active assay as set by activateAssay().
overwrite	Logical value. Must be TRUE to allow overwriting.
...	Used to absorb deprecated arguments or functions.
expr_mtr	A matrix in which the rownames correspond to the feature names and the column names correspond to the barcodes.

Value

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

Examples

library(SPATA2)
library(tidyverse)

data("example_data")

object <- example_data$object_UKF275T_diet

library(Seurat)

scaled_mtr <-
 CreateSeuratObject(getCountMatrix(object)) %>%
 NormalizeData() %>%
 ScaleData() %>%
 GetAssayData(layer = "scale.data")

object <- addProcessedMatrix(object, proc_mtr = scaled_mtr, mtr_name = "scaled")

p1 <- plotSurface(object, color_by = "METRN")

object <- activateMatrix(object, mtr_name = "scaled")

p2 <- plotSurface(object, color_by = "METRN")

plot(p1)
plot(p2)

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