asSPATA2: Transform to 'spata2' object object

In kueckelj/SPATA2: A Toolbox for Spatial Gene Expression Analysis

Transform to spata2 object object

Description

Transforms input object to object of class spata2 object.

Usage

asSPATA2(object, ...)

## S4 method for signature 'giotto'
asSPATA2(
  object,
  sample_name,
  coordinates,
  image_ebi,
  spatial_method,
  transfer_meta_data = TRUE,
  verbose = TRUE,
  ...
)

## S4 method for signature 'Seurat'
asSPATA2(
  object,
  sample_name,
  spatial_method,
  assay_name = "Spatial",
  image_name = "slice1",
  transfer_meta_data = TRUE,
  transfer_dim_red = TRUE,
  count_mtr_name = "counts",
  scaled_mtr_name = "scale.data",
  verbose = TRUE
)

## S4 method for signature 'AnnDataR6'
asSPATA2(
  object,
  sample_name,
  count_mtr_name = "counts",
  normalized_mtr_name = "normalized",
  scaled_mtr_name = "scaled",
  transfer_meta_data = TRUE,
  transfer_dim_red = TRUE,
  image_name = NULL,
  verbose = TRUE
)

Arguments

object	An object of either one of the following classes: Seurat, SingleCellExperiment, AnnDataR6
...	Additional arguments given to initiateSpataObject_CountMtr().
sample_name	A character string specifying the name of the sample
spatial_method	Character value. The name of the spatial method that underlies the experiment. Must be one of validSpatialMethods(). Defaults to 'Unknown'.
transfer_meta_data	Logical or character. Specifies if meta data, e.g clustering, from the input object is transferred to the output object. If TRUE, all variables of the meta data.frame are transferred. If character, named variables are transferred. If FALSE, none are transferred.
verbose	Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)
transfer_dim_red	A logical specifying whether to transfer dimensional reduction data (PCA, UMAP, tSNE) from the input object to the output object.
count_mtr_name	A character string specifying the name of the count matrix
scaled_mtr_name	A character string specifying the name of the scaled matrix
normalized_mtr_name	A character string specifying the name of the normalized matrix (anndata only currently)

Value

An object of class spata2 object.

kueckelj/SPATA2 documentation built on March 16, 2024, 10:25 a.m.