Read Visium output into spe

Read Visium output into spe

Usage

readVisium(
  dir,
  sample_id = "sample01",
  count = NULL,
  coord = NULL,
  image = NULL,
  scale_factors = NULL,
  feature_type = "Gene Expression"
)

Arguments

dir

directory containing the Visium files

sample_id

Name of the sample.

count

Name of the h5 file with the count assay.

coord

Name of the csv file with the tissue coordinates

image

Names of the image files.

scale_factors

Names of the scale factors file

feature_type

Feature type to retain. Defaults to "Gene Expression" to exclude non-gene features. Set to NULL to keep all features.