TreeIndex-methods: Subset TreeIndex

In jkanche/TreeSE: R/Bioconductor package to interactively explore and visualize single cell RNA-seq datasets with hierarhical annotations

Description

Subset TreeIndex

Generic method to get nodes at a tree level

Method to get nodes at a tree level

Generic method for possible node states

Method to get possible node states a node state is 0 if removed, 1 if expanded to show children & 2 if counts are aggregated to the node

Generic method to split the tree

splitAt divides the TreeIndex into groups defined by the level, node selections and filters(start, end)

Show the TreeIndex object

Usage

## S4 method for signature 'TreeIndex,ANY,ANY,ANY'
x[i, j, ..., drop = FALSE]

getNodes(x, ...)

## S4 method for signature 'TreeIndex'
getNodes(x, selectedLevel = NULL)

getNodeStates(x)

## S4 method for signature 'TreeIndex'
getNodeStates(x)

splitAt(x, ...)

## S4 method for signature 'TreeIndex'
splitAt(
  x,
  selectedLevel = 3,
  selectedNodes = NULL,
  start = 1,
  end = NULL,
  format = "list"
)

## S4 method for signature 'TreeIndex'
show(object)

Arguments

x	TreeIndex object
i, j	indices to subset or keep
...	other parameters
drop	drop the dimensions of the object. defaults to FALSE
selectedLevel	tree level to select nodes from
selectedNodes	used to set states on individual nodes to define a cut on the tree
start, end	indices to filter nodes by
format	return format can be one of "list" or "TreeIndex"
object	TreeIndex object

Value

a 'TreeIndex' subset object

a generic

levels at node cut

node state

node states

a generic

a 'TreeIndex' object or type set in format

object description of the 'TreeIndex' object

Examples

library(metagenomeSeq)
data(mouseData)
counts <- MRcounts(mouseData)
hierarchy <- fData(mouseData)
tree <- TreeIndex(hierarchy)
getNodes(tree)
library(metagenomeSeq)
data(mouseData)
counts <- MRcounts(mouseData)
hierarchy <- fData(mouseData)
tree <- TreeIndex(hierarchy)
getNodes(tree)
 
library(metagenomeSeq)
data(mouseData)
counts <- MRcounts(mouseData)
hierarchy <- fData(mouseData)
tree <- TreeIndex(hierarchy)
splitAt(tree)

 
library(metagenomeSeq)
data(mouseData)
counts <- MRcounts(mouseData)
hierarchy <- fData(mouseData)
tree <- TreeIndex(hierarchy)
splitAt(tree)

jkanche/TreeSE documentation built on Oct. 1, 2021, 8:31 p.m.