run.scanpy: Wraper for running scanpy pipeline
In Japrin/scPip: pipeline for scRNA-seq data analysis

run.scanpy

R Documentation

Wraper for running scanpy pipeline

Description

Wraper for running scanpy pipeline

Usage

run.scanpy(
  adata,
  out.prefix,
  gene.exclude.df,
  n.top = 1500,
  opt.res = "1",
  aid = "PRJ",
  plot.rd = c("umap"),
  opt.npc = 15,
  ncores = 16,
  res.test = seq(0.1, 2.4, 0.1),
  cor.var = c("S_score", "G2M_score", "DIG.Score", "percent.mito"),
  ncell.deg = 1500,
  do.deg = F,
  hvg.batch.minNCells = 100,
  use.harmony = T,
  method.integration = NULL,
  specie = "human",
  gene.mapping.table = NULL,
  res.addition = NULL,
  run.stage = 100
)

Arguments

`adata`	object of `AnnData`
`out.prefix`	character; output prefix
`gene.exclude.df`	data.frame; gene blak list. Required column: seu.id.
`n.top`	integer; number of top genes. (default: 1500)
`opt.res`	character; optimal resolution (default: "1")
`aid`	character; an ID (default: "PRJ")
`plot.rd`	character vector; reducedDimNames used for plots (default: c("umap"))
`opt.npc`	integer; optimal number of principal componets to use (default: 15)
`ncores`	integer; number of CPU cores to use (default: 16)
`res.test`	double; resolutions to test (default: seq(0.1,2.4,0.1) )
`cor.var`	character vector; Subset of c("S_score","G2M_score","DIG.Score","ISG.Score","percent.mito") or NULL. (default: c("S_score","G2M_score","DIG.Score","percent.mito")).
`ncell.deg`	integer; number of cell to downsample. used in the differentially expressed gene analysis. (default: 1500)
`do.deg`	logical; whether perform the differentially expressed gene analysis. (default: FALSE)
`hvg.batch.minNCells`	integer; required minimum number of cells in each batch. Batch with < hvg.batch.minNCells will not be used for HVG finding. (default: 100)
`use.harmony`	logical; whether use the harmony method. (default: TRUE)
`method.integration`	character; integration method. (default: NULL)
`specie`	character; specie, one of "human", "mouse". (default: "human")
`gene.mapping.table`	data.table; used for gene ID conversion. (default: NULL)
`res.addition`	character vector; additional resolution parameters. Internally, resolutions from 0.1 to 2.4 will be used. (default: NULL)
`run.stage`	integer; running stage. (default: 100)