saveConosForScanPy: Save Conos object on disk to read it from ScanPy

saveConosForScanPyR Documentation

Save Conos object on disk to read it from ScanPy

Description

Save Conos object on disk to read it from ScanPy

Usage

saveConosForScanPy(
  con,
  output.path,
  hdf5_filename,
  metadata.df = NULL,
  cm.norm = FALSE,
  pseudo.pca = FALSE,
  pca = FALSE,
  n.dims = 100,
  embedding = TRUE,
  alignment.graph = TRUE,
  verbose = FALSE
)

Arguments

con

conos object

output.path

path to a folder, where intermediate files will be saved

hdf5_filename

name of HDF5 written with ScanPy files. Note: the rhdf5 package is required

metadata.df

data.frame with additional metadata with rownames corresponding to cell ids, which should be passed to ScanPy (default=NULL) If NULL, only information about cell ids and origin dataset will be saved.

cm.norm

boolean Whether to include the matrix of normalised counts (default=FALSE).

pseudo.pca

boolean Whether to produce an emulated PCA by embedding the graph to a space with 'n.dims' dimensions and save it as a pseudoPCA (default=FALSE).

pca

boolean Whether to include PCA of all the samples (not batch corrected) (default=FALSE).

n.dims

numeric Number of dimensions for calculating PCA and/or pseudoPCA (default=100).

embedding

boolean Whether to include the current conos embedding (default=TRUE).

alignment.graph

boolean Whether to include graph of connectivities and distances (default=TRUE).

verbose

boolean Whether to use verbose mode (default=FALSE)

Value

AnnData object for ScanPy, saved to disk

See Also

The rhdf5 package documentation here: <https://www.bioconductor.org/packages/release/bioc/html/rhdf5.html>


conos documentation built on April 12, 2022, 1:06 a.m.