ccOptions-class: Class "ccOptions"

In categoryCompare: Meta-analysis of high-throughput experiments using feature annotations

Description

These objects store the various options required by categoryCompare for actually making comparisons and generating output.

Objects from the Class

Objects can be created by calls of the form new("ccOptions", listNames=c('list1','list2',etc)). This is the minimum call required, and will generate a ccOptions object where comparisons are assumed between all the lists supplied. See the examples section for more examples of how to initialize new objects.

Slots

listNames:

Object of class "character" The actual names of the various datasets defined in the ccData object

compareNames:

Object of class "character" Which lists to compare, each entry should be a comma separated list

compareIndx:

Object of class "list" List indices for each of the comparison, not usually set by the user. Generated automatically.

compareColors:

Object of class "character" For graphical and tabular output each comparison can be colored. Should be one color for each comparison. Can be either an n by 3 matrix of rgb triples, or a character vector of hexadecimal color codes, or character vector of color names ('red','green','blue', etc)

cssClass:

Object of class "character" Classnames used when generating HTML tables to color entries. Generated automatically upon initialization, or modifying compareNames

outType:

Object of class "character" Sets the type of output generated by ccTables. Valid types are "html", "text", "rcy3" or "none", default is "text" when the ccOptions object is initialized without an outType specified.

Methods

compareColors

signature(object = "ccOptions"): ...

compareColors<-

signature(object = "ccOptions"): ...

compareIndx

signature(object = "ccOptions"): ...

compareNames

signature(object = "ccOptions"): ...

compareNames<-

signature(object = "ccOptions"): ...

cssClass

signature(object = "ccOptions"): ...

listNames

signature(object = "ccOptions"): ...

listNames<-

signature(object = "ccOptions"): ...

outType

signature(object = "ccOptions"): ...

outType<-

signature(object = "ccOptions"): ...

Author(s)

Robert M Flight

Examples

showClass("ccOptions")
## A very basic "ccOptions" for a comparison of two sets of data, "list1" and "list2"
c1 <- new("ccOptions", listNames=c('list1','list2'))
c1

## Now lets get a little more complicated
c1 <- new("ccOptions", listNames=c('list1','list2'),
compareNames=c('list1,list2','list1,list3'), compareColors=c('red','blue'))
c1

# set the type of output you want to eventually produce
c1 <- new("ccOptions", listNames=c('list1','list2'), outType='html')
c1

c1 <- new("ccOptions", listNames=c('list1','list2'), outType=c('html','text','none'))
c1

## Using RGB colors
ccCols <- matrix(c(255,0,0, 0,0,255), nrow=2, ncol=3)
ccCols <- rgb(ccCols, maxColorValue=255)
c1 <- new("ccOptions", listNames=c('list1','list2','list3'),
compareNames=c('list1,list2','list1,list3'), compareColors=ccCols)

## Using Hex colors
c1 <- new("ccOptions", listNames=c('list1','list2','list3'),
compareNames=c('list1,list2','list1,list3'), compareColors=c('#FF0000','#0000FF'))
c1

## or even using a color palette from R.
## Note that you need at least enough colors to cover all of individual and
## possible permutations (n!) if you use compareNames='all'
c1 <- new("ccOptions", listNames=c('list1','list2','list3'),
compareNames=c('list1,list2','list1,list3'), compareColors=rainbow(4))
c1

categoryCompare documentation built on Nov. 8, 2020, 5:59 p.m.