TreeViz-methods: show object

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

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

## 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

• show,TreeViz-method:

• aggregateTree:

• aggregateTree,TreeViz-method:

• register,TreeViz-method:

• plot,TreeViz,ANY-method:

Examples

 
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.