ngchmVersion2-class: Class representing ngchmVersion2 object
In MD-Anderson-Bioinformatics/NGCHM-R: Next Generation Clustered Heat Maps

ngchmVersion2-class

R Documentation

Class representing ngchmVersion2 object

Description

Class representing ngchmVersion2 object

Slots

name: The name under which the NGCHM will be saved to the NGCHM server.
version: Integer version number (default: 2)
format: (default: "original")
uuid: character
baggage: optCharacter
inpDir: character
outDir: character
saveDir: (default: tempdir())
propFile: (default: "chm.properties")
layers: List of data layers
colormaps: Color map
rowMenu: optList
colMenu: optList
datasets: optList
dialogs: optList
tags: optCharacter
elementMenu: optList
rowTypeFunctions: optList
colTypeFunctions: optList
elementTypeFunctions: optList
axisTypes: optList
css: optList
extrafiles: optCharacter
extrascripts: optCharacter
properties: optList
overviews: optList
javascript: optList
rowOrder: A vector, dendrogram, or function specifying the CHM row order
rowDist: Distance method to use by default RowOrder. (default: "correlation", which is 1 minus the Pearson correlation among the rows.)
rowAgglom: Agglomeration method to use by default RowOrder. Choices are those from stats::hclust. (default: "ward.D2")
colOrder: A vector, dendrogram, or function specifying the CHM column order.
colDist: Distance method to use by default ColOrder. (default: "correlation", which is 1 minus the Pearson correlation among the cols.)
colAgglom: Agglomeration method to use by default ColOrder. Choices are those from stats::hclust. (default: "ward.D2")
rowOrderMethod: character (default: "User")
colOrderMethod: character (default: "User")
rowCutLocations: Explicit list of row cut locations. If specified, rowTreeCuts is set to NULL.
rowTreeCuts: Number of tree cuts for row. If specified, rowCutLocations is set to NULL.
rowCutWidth: Width of row cuts (default: 5 rows)
rowTopItems: optCharacter
rowDisplayLength: optInteger
rowDisplayAbbreviation: optCharacter
colCutLocations: Explicit list of col cut locations. If specified, colTreeCuts is set to NULL.
colTreeCuts: Number of tree cuts for col. If specified, colCutLocations is set to NULL.
colCutWidth: Width of col cuts (defautl: 5 columns)
colTopItems: optCharacter
colDisplayLength: optInteger
colDisplayAbbreviation: optCharacter
rowMeta: optList
colMeta: optList
rowCovariateBars: optList
colCovariateBars: optList
relatedLinks: optList
relatedGroups: optList
templates: optList
width: default: 500
height: default: 500