Initiate spata object from scaled expression matrix — initiateSpataObject

Default function for any spatial related experiment whoose output is an already processed expression/intensity matrix. See details for more information.

initiateSpataObject_ExprMtr(
  coords_df,
  expr_mtr,
  sample_name,
  spatial_method = "Unknown",
  count_mtr = NULL,
  mtr_name = "scaled",
  image = NULL,
  image_class = "HistologyImage",
  image_object = NULL,
  directory_spata = NULL,
  combine_with_wd = FALSE,
  gene_set_path = NULL,
  k = 50,
  nn = NULL,
  runPca = list(n_pcs = 30),
  runTsne = list(tsne_perplexity = 30),
  runUmap = list(),
  verbose = TRUE
)

Arguments

coords_df

Data.frame containing information about the positions of all barcode-spots in form of a numeric x- and y-variable. The key-variable barcodes needs to be of type character and must be identical to the column names of the input matrix.

expr_mtr

A numeric matrix. The expression matrix to be used.

sample_name

Character value. Denotes the name of the sample you are analyzing with the spata-object. The future input for SPATA's of_sample-argument.

image

An Image of the sample that can be displayed as the surface plot's background.

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.

k, nn

Numeric value. Given to argument k of function RANN::nn2(): Determines to maximum number of nearest neighbours to compute. (nn is deprecated.)

Value

A spata2 object.

Details

After initiating the spata2 object PCA is performed via irlba::prcomp_irlba() and clustering is done via RANN::nn2(). (Use addFeatures() to add any clustering results of your own analysis.) Additional dimensional reduction is performed via Rtsne::Rtsne() and umap::umap().

Note that this function initiates a spata2 object that does not contain a count-matrix! You can add a count-matrix manually using setCountmatrix(). As long as there is none functions that need a count-matrix will throw an error telling you that no count matrix could be found.