process_counts: process counts

In patrickCNMartin/Vesalius: Vesalius: Dissecting Tissue Anatomy from Spatial Transcriptomic Data

process counts

Description

pre-process count matrices

Usage

process_counts(
  counts,
  assay,
  method = "log_norm",
  use_count = "raw",
  nfeatures = 2000,
  min_cutoff = "q5",
  verbose = TRUE
)

Arguments

counts	count matrix in the form of a sparse matrix
assay	character string describing the assay that is being pre-processed in the vesaliusObject or vesalius_assay
method	character string describing which normalisation method to use. One of the following "log_norm", "SCT", "TFIDF", "none".
use_count	string describing which counts should be used for the generating emebddings. Default = "raw".
nfeatures	numeric describing the number of variable features to use.
min_cutoff	only used when dimensionality reduction method is LSI or LSI_UMAP cutoff for feature to be included in the VariableFeatures for the object.
verbose	logical - progress messages outputed or not

Details

The 'use_count' argument specifies which count matrix should be used for normalization. This argument is only necessary if you use a custom normalised count matrix. In this case, set this argument to the name you gave your count matrix (see add_counts) and 'generate_embeddings' will skip the normalization and use your custom count matrix to generate image embeddings.

patrickCNMartin/Vesalius documentation built on April 17, 2025, 11:31 p.m.