TreeViz-methods: show object

Description Usage Arguments Value Functions Examples

Description

show object

Method to aggregate a TreeViz object

Method to aggregate a TreeViz object

Generic method to register data to the epiviz data server

plot tree from TreeViz

Usage

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

aggregateTree(x, ...)

## S4 method for signature 'TreeViz'
aggregateTree(
  x,
  selectedLevel = 3,
  selectedNodes = NULL,
  aggFun = colSums,
  start = 1,
  end = NULL,
  by = "row",
  format = "TreeViz"
)

## S4 method for signature 'TreeViz'
register(object, tree = "row", columns = NULL, ...)

## S4 method for signature 'TreeViz,ANY'
plot(x, y)

Arguments

object

The object to register to data server

x

treeviz object

...

Additional arguments passed to object constructors

selectedLevel

level to select nodes from

selectedNodes

used to set states on individual nodes to define a cut on the tree

aggFun

aggregate function to use, by default colSums if by="row", rowSums if by="col"

start, end

indices to filter nodes

by

"row" to aggregate the TreeIndex on rowData, "col" to aggregate TreeIndex on colData

format

return format can be one of "counts" or "TreeViz"

tree

Is tree over rows or columns of the object (default: "row")

columns

Name of columns containing data to register

y

none

Value

describe a TreeIndex object

a generic

a Treeviz object or type specified by format

An EpivizTreeData-class object

Dataframe containing cluster information at different resolutions

Functions

Examples

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library(metagenomeSeq)
data(mouseData)
counts <- MRcounts(mouseData)
hierarchy <- fData(mouseData)
tree <- TreeIndex(hierarchy)
mbiome <- TreeViz(SimpleList(counts=counts), rowData=tree)
aggregateTree(mbiome)

 
library(metagenomeSeq)
data(mouseData)
counts <- MRcounts(mouseData)
hierarchy <- fData(mouseData)
tree <- TreeIndex(hierarchy)
mbiome <- TreeViz(SimpleList(counts=counts), rowData=tree)
aggregateTree(mbiome)


library(metagenomeSeq)
data(mouseData)
counts <- MRcounts(mouseData)
hierarchy <- fData(mouseData)
tree <- TreeIndex(hierarchy)
mbiome <- TreeViz(SimpleList(counts=counts), rowData=tree)
plot(mbiome)

HCBravoLab/palmtree documentation built on Dec. 17, 2021, 10:25 p.m.