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.