TreeIndex-methods: Subset TreeIndex

Description Usage Arguments Value Examples

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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
## 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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
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)

HCBravoLab/scTreeViz documentation built on Dec. 17, 2021, 10:26 p.m.