chmNew: Create a new NGCHM.

Description Usage Arguments Value See Also Examples

View source: R/functions.R

Description

This function creates a Next Generation Clustered Heat Map (NGCHM) object in memory. Additional parameters will be added to the new NGCHM (see chmAdd). The bare NGCHM needs at least one data layer added to it before it can be compiled.

Usage

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chmNew(name, ..., rowOrder = chmDefaultRowOrder, rowDist = "correlation",
  rowAgglom = "ward.D2", colOrder = chmDefaultColOrder,
  colDist = "correlation", colAgglom = "ward.D2", rowAxisType = NULL,
  colAxisType = NULL, rowCovariates = NULL, colCovariates = NULL,
  format = "original", overview = c())

Arguments

name

The name under which the NGCHM will be saved to the NGCHM server.

...

Zero or more initial objects to include in the NGCHM (see chmAdd).

rowOrder

A vector, dendrogram, or function specifying the CHM row order.

rowDist

Distance method to use by default RowOrder

rowAgglom

Agglomeration method to use by default RowOrder

colOrder

A vector, dendrogram, or function specifying the CHM column order.

colDist

Distance method to use by default ColOrder

colAgglom

Agglomeration method to use by default ColOrder

rowAxisType

The type(s) of the row labels (default: None).

colAxisType

The type(s) of the column labels (default: None).

rowCovariates

Covariate(Bar)(s) to add to the rows (default: None).

colCovariates

Covariate(Bar)(s) to add to the columns (default: None).

format

The format of NGCHM to produce (default: 'original').

overview

The format(s) of overview image(s) to create (default: None).

Value

An object of class ngchm

See Also

ngchm-class

ngchmServer-class

chmAdd

chmAddAxisType

chmAddCovariateBar

chmAddProperty

chmAddOverview

chmInstall

chmExportToFile

chmExportToPDF

Examples

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mychm <- chmNew ("test_chm")

bmbroom/NGCHMR documentation built on July 28, 2018, 11:17 a.m.