make.p2.app {pagoda2}

Generate a Rook Server app from a 'Pagoda2' object. This generates a 'pagoda2' web object from a 'Pagoda2' object by automating steps that most users will want to run. This function is a wrapper about the 'pagoda2' web constructor. (Advanced users may wish to use that constructor directly.)

Description

Generate a Rook Server app from a 'Pagoda2' object. This generates a 'pagoda2' web object from a 'Pagoda2' object by automating steps that most users will want to run. This function is a wrapper about the 'pagoda2' web constructor. (Advanced users may wish to use that constructor directly.)

Usage

make.p2.app(
  r,
  dendrogramCellGroups,
  additionalMetadata = list(),
  geneSets,
  show.depth = TRUE,
  show.batch = TRUE,
  show.clusters = TRUE,
  appname = "Pagoda2 Application",
  innerOrder = NULL,
  orderDend = FALSE,
  appmetadata = NULL
)

Arguments

r

a 'Pagoda2' object

dendrogramCellGroups

a named factor of cell groups, used to generate the main dendrogram, limits zoom in

additionalMetadata

a list of metadata other than depth, batch and cluster that are automatically added (default=list())

geneSets

a list of genesets to show

show.depth

boolean Include depth as a metadata row (default=TRUE)

show.batch

boolean Include batch as a metadata row (default=TRUE)

show.clusters

boolean Include clusters as a metadata row (default=TRUE)

appname

character Application name (default="Pagoda2 Application")

innerOrder

Ordering of cells inside the clusters provided in dendrogramCellGroups (default=NULL). This should be one of "odPCA", "reductdist", "graphbased", "knn". Defaults to NULL

orderDend

boolean Whether to order dendrogram (default=FALSE)

appmetadata

a 'pagoda2' web application metadata (default=NULL)

Value

a 'pagoda2' web object that presents a Rook compatible interface