transformSeuratToSpata: Transform seurat-object to spata-object
In kueckelj/SPATA2: A Toolbox for Spatial Gene Expression Analysis

transformSeuratToSpata

R Documentation

Transform seurat-object to spata-object

Description

This function provides a convenient way to transform your seurat-object into a spata-object while maintaining as much analysis progress as possible. See details for more information.

Usage

transformSeuratToSpata(
  seurat_object,
  sample_name,
  method = "spatial",
  coords_from = "pca",
  assay_name = NULL,
  assay_slot = NULL,
  image_name = NULL,
  gene_set_path = NULL,
  verbose = TRUE
)

Arguments

`seurat_object`	A valid seurat object.
`sample_name`	Character value. Future input for SPATA's `of_sample`-argument.
`method`	Character value. Determines the data slots from which to compile the spata-object. 'spatial' Denotes that the data to be used derived from spatial experiments. 'single_cell' Denotes that the data to be used derived from single cell experiments.
`coords_from`	Character value. Either 'pca', 'tsne' or 'umap'. Only relevant if `method` was set to 'single_cell'. Denotes the slot from which to take the surrogate coordinates. If the specified data ist not found the slot @coordinates will contain an empty data.frame and has to be set manually with `setCoordsDf()`.
`assay_name`	Character value. Denotes the assay from which to transfer the data. If the seurat-object contains only one assay `assay_name` = NULL makes `transformSeuratToSpata()` choose the only one found.
`assay_slot`	Character value. Denotes the slot of the seurat-object's assay object from which to transfer the expression matrix (the count matrix is always taken from slot `@counts`). Either 'data' or 'scale.data'. If set to NULL the functions checks both options for validity. If both slots contain valid expression matrix candidates it defaults to 'scale.data'.
`gene_set_path`	Character value (or NULL). Specifies the path to a .RDS-file containing a data.frame that is to be used as input for slot @used_genesets. Must have the character-variables 'ont': The gene set names. 'gene': The belonging gene names. If set to NULL the default gene-set data.frame will used. Run `?gsdf` to get more information.
`verbose`	Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)

Details

This function assembles a spata-object from the data it finds in the provided seurat-object. This always includes gene count- and expression-matrices as well as dimensional reduction data like PCA, UMAP and TSNE. Whenever transformSpataToSeurat() does not find anything it well tell you via a warning message or an error message if the missing data is essential to the spata-object. You might have to run certain functions afterwards with the obtained SPATA-object. (e.g. did not find UMAP data in seurat-object -> runUmap()).

If your seurat-object contains more than one assay-object or more than one SpatialImage-object you need to specify the respective objects by name using the arguments assay_name and image_name. If the assay you denoted with assay_name contains more than one valid expression matrix you need to specify the one you want to use as the spata-object's scaled_mtr using the argument assay_slot.

Seurat-objects containing data derived from spatial experiments (method = 'spatial'):

If you specify argument method as 'spatial' transformSeuratToSpata() assumes that the provided seurat-object contains a SpatialImage-object in slot @images from which it will extract the coordinates and the histology image.

Seurat-objects containing data derived from spatial experiments (method = 'single_cell'):

If you specify argument method as 'single_cell' transformSeuratToSpata() uses either tsne or umap embedding as surrogate coordinates.