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",
  pixel_to_micron = TRUE
)

Arguments

dir

directory containing the Visium files

sample_id

Name of the sample.

count

Name of the h5 file with the count assay.

coord

Path to the tissue coordinates file (csv or parquet), or a data.frame of coordinates (rownames = barcodes) with columns 'pxl_col_in_fullres' and 'pxl_row_in_fullres'.

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.

pixel_to_micron

Logical. If TRUE (default), convert the spot coordinates from full-resolution pixels to microns using 'spot_diameter_fullres' from the scale factors file, and store the conversion factor in metadata(spe)$um_per_pixel. Set to FALSE to keep the coordinates in pixels (previous behaviour).