seuratObjectToViewer: seuratObjectToLocalViewer This function creates a shiny...

In decusInLabore/biologicViewerSC: PKG_TITLE

seuratObjectToLocalViewer This function creates a shiny single-cell viewer based on a Seurat single-cell object.

Description

seuratObjectToLocalViewer

This function creates a shiny single-cell viewer based on a Seurat single-cell object.

Usage

seuratObjectToViewer(
  params = NULL,
  project_id = "testApp",
  projectPath = "./",
  OsC = NULL,
  dataMode = "MySQL",
  host = "dbHostURL",
  dbname = "dbname_db",
  db.pwd = "dbAdminPassword",
  db.user = "boeings",
  appDomains = c("shiny-bioinformatics.crick.ac.uk", "10.%"),
  geneDefault = NULL,
  dfExpr = NULL,
  clusterNameColumn = "clusterName",
  sampleNameColumn = "sampleName",
  seuratAssayToUse = "RNA",
  defaultSplitOption = NULL
)

Arguments

params	A parameter list created by the biologicViewerSC::scanObjParams function.
project_id	A project ID string
projectPath	A path into which the shiny app will be deposited.
OsC	A Seurat object
dataMode	"MySQL" or "SQLite". This parameter determines whether a remote MySQL database ("MySQL") or a local database ("SQLite") is used
host	Host url
dbname	Database name
db.pwd	Database password
db.user	Database username
geneDefault	Default gene string
dfExpr	Dataframe containing expression data
clusterNameColumn	Column name of the sample name column
sampleNameColumn	Column name of the cluster name column

Value

No return. A shiny single-cell app will be created.

decusInLabore/biologicViewerSC documentation built on Nov. 29, 2024, 11:46 a.m.