saveConosForScanPy {conos}

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>