import_scanpy_h5: Imports a scanpy h5 object

In scfurl/m3addon: This package adds to the popular "monocle3"

Description

read in a Scanpy h5 object.

Usage

import_scanpy_h5(
  file,
  raw = TRUE,
  rowname_col = "GeneID",
  gene_short_name_col = "GeneName",
  colors = NULL,
  PCA = T,
  UMAP = TRUE,
  neighbors = T,
  var_features = T
)

Arguments

file	h5 scanpy object
raw	data contained in the raw slot - See scanpy documentation for more info
rowname_col	feature column for rownames (should contain unique values - suggest ENSID)
gene_short_name_col	feature column for gene_short_name (suggest Symbol)
colors	name or names of color palatte to import
exprs_bin	Boolean whether to bin genes by mean expression
exprs_cuts	Numeic indicating number of bins if using exprs_bin

Value

Updated cell_data_set object

scfurl/m3addon documentation built on Aug. 9, 2021, 5:30 p.m.