chmNew: Create a new NGCHM.

In MD-Anderson-Bioinformatics/NGCHM-R: Next Generation Clustered Heat Maps

Create a new NGCHM.

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. This function requires git to be installed.

Usage

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",
  rowGapLocations = NULL,
  rowGapWidth = 5,
  colGapLocations = NULL,
  colGapWidth = 5,
  overview = c(),
  logLevel = "INFO",
  logFile = NULL
)

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').
rowGapLocations	Locations for row gaps. Specify as a list of integers or chmTreeGaps() function.
rowGapWidth	Width of row gaps (default: 5 rows)
colGapLocations	Locations for col gaps. Specify as a list of integers or chmTreeGaps() function.
colGapWidth	Width of col gaps (default: 5 cols)
overview	The format(s) of overview image(s) to create (default: None).
logLevel	The level of logs to output
logFile	The file to which logs should be output

Value

An object of class ngchm

See Also

ngchm

ngchmServer

chmAdd()

chmAddAxisType()

chmAddCovariateBar()

chmAddProperty()

chmAddOverview()

chmInstall()

chmExportToFile()

chmExportToPDF()

chmExportToHTML()

Examples

mychm <- chmNew("test_chm")
mychm <- chmNew("test_chm", rowGapLocations = c(3, 5))
mychm <- chmNew("test_chm", rowGapLocations = chmTreeGaps(4))
mychm <- chmNew("test_chm", rowGapWidth = 3)

MD-Anderson-Bioinformatics/NGCHM-R documentation built on April 1, 2024, 12:34 p.m.