Initiate a spata2 object from example data sets — initiateSpataObject

Creates and returns an object of class spata from the example data sets provided by the package SeuratData. See details for more.

initiateSpataObject_Examples(
  data_set = "stxBrain",
  type = "anterior1",
  force = FALSE,
  gene_set_path = NULL,
  SCTransform = FALSE,
  NormalizeData = list(normalization.method = "LogNormalize", scale.factor = 1000),
  FindVariableFeatures = list(selection.method = "vst", nfeatures = 2000),
  ScaleData = TRUE,
  RunPCA = list(npcs = 60),
  FindNeighbors = list(dims = 1:30),
  FindClusters = list(resolution = 0.8),
  RunTSNE = TRUE,
  RunUMAP = list(dims = 1:30),
  verbose = TRUE
)

Arguments

data_set

Character value. The data-set from which to create the spata2 object. Currently only 'stxBrain' is available. Additional datat sets will be added shortly.

type

Given to argument type of funciton SeuratData::LoadData().

force

Logical. If set to TRUE, the function installs all requirements (packages, data sets) automatically without requesting any further permission. If set to FALSE, the function stops with an informative error message when it encounters missing installations.

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.

SCTransform

A named list of arguments given to Seurat::SCTransform(), TRUE or FALSE.

NormalizeData

A named list of arguments given to Seurat::NormalizeData(), TRUE or FALSE.

FindVariableFeatures

A named list of arguments given to Seurat::FindVariableFeatures(), TRUE or FALSE.

ScaleData

A named list of arguments given to Seurat::ScaleData(), TRUE or FALSE.

Hint: If set to TRUE or the argument-list provided does not specify the argument features input for argument features is set to base::rownames(seurat_object).

RunPCA

A named list of arguments given to Seurat::RunPCA(), TRUE or FALSE.

FindNeighbors

A named list of arguments given to Seurat::FindNeighbors(), TRUE or FALSE.

FindClusters

A named list of arguments given to Seurat::FindClusters(), TRUE or FALSE.

RunTSNE

A named list of arguments given to Seurat::RunTSNE(), TRUE or FALSE.

RunUMAP

A named list of arguments given to Seurat::RunUMAP(), TRUE or FALSE.

verbose

Logical. If set to TRUE informative messages regarding the computational progress will be printed.

(Warning messages will always be printed.)

Value

A spata2 object.

Details

The loading and preprocessing of the spata2 object currently relies on the Seurat-package. Before any pre processing function is applied mitochondrial and stress genes are discarded. For more advanced users the arguments above starting with a capital letter allow to manipulate the way the spata2 object is processed. For all of these arguments apply the following instructions:

If set to FALSE the processing function is skipped.
If set to TRUE the respective function is called with it's default argument settings. Note: RunUMAP() needs additional input!
If a named list is provided the respective function is called whereby the named list will provide the argument-input (the Seurat object to be constructed must not be named and will be passed to every function as the first argument!!!.)

Note that certain listed functions require previous functions! E.g. if RunPCA is set to FALSE RunTSNE() will result in an error. (base::tryCatch() will prevent the function from crashing but the respective slot is going to be empty.) Skipping functions might result in an incomplete spata2 object. Use validateSpataObject() after initiating it in order to see which slots are valid and which are not.