show,TreeViz-method {scTreeViz} | R Documentation

## show object

### 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)

[Package scTreeViz version 1.0.0 Index]