View source: R/read10xVisiumWrapper.R
read10xVisiumWrapper | R Documentation |
This function expands SpatialExperiment::read10xVisium()
to include
analysis results from SpaceRanger by 10x Genomics as well as add information
needed by run_app()
to visualize the data with the spatialLIBD
shiny
web application.
read10xVisiumWrapper(
samples = "",
sample_id = paste0("sample", sprintf("%02d", seq_along(samples))),
type = c("HDF5", "sparse"),
data = c("filtered", "raw"),
images = c("lowres", "hires", "detected", "aligned"),
load = TRUE,
reference_gtf = NULL,
chrM = "chrM",
gtf_cols = c("source", "type", "gene_id", "gene_version", "gene_name", "gene_type"),
verbose = TRUE
)
samples |
Passed to |
sample_id |
Passed to |
type |
Passed to |
data |
Passed to |
images |
Passed to |
load |
Passed to |
reference_gtf |
A |
chrM |
A |
gtf_cols |
A |
verbose |
A |
A SpatialExperiment object with the
clustering and dimension reduction (projection) results from SpaceRanger by
10x Genomics as well as other information used by run_app()
for visualzing
the gene expression data.
Other Utility functions for reading data from SpaceRanger output by 10x
Genomics:
add10xVisiumAnalysis()
,
read10xVisiumAnalysis()
## See 'Using spatialLIBD with 10x Genomics public datasets' for
## a full example using this function.
if (interactive()) {
browseVignettes(package = "spatialLIBD")
}
## Note that ?SpatialExperiment::read10xVisium doesn't include all the files
## we need to illustrate read10xVisiumWrapper().
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.