Class "VENNset"

Container for storing Venn intersect results created by the overLapper function. The setlist slot stores the original label sets as vectors in a list; intersectmatrix organizes the label sets in a present-absent matrix; complexitylevels represents the number of comparisons considered for each comparison set as vector of integers; and vennlist contains the Venn intersect vectors.

Objects from the Class

Objects can be created by calls of the form new("VENNset", ...).

Slots

setlist:

Object of class "list": list of vectors

intersectmatrix:

Object of class "matrix": binary matrix

complexitylevels:

Object of class "integer": vector of integers

vennlist:

Object of class "list": list of vectors

Methods

as.list

signature(x = "VENNset"): coerces VENNset to list

coerce

signature(from = "list", to = "VENNset"): as(list, "VENNset")

complexitylevels

signature(x = "VENNset"): extracts data from complexitylevels slot

intersectmatrix

signature(x = "VENNset"): extracts data from intersectmatrix slot

length

signature(x = "VENNset"): returns number of original label sets

names

signature(x = "VENNset"): extracts slot names

setlist

signature(x = "VENNset"): extracts data from setlist slot

show

signature(object = "VENNset"): summary view of VENNset objects

vennlist

signature(x = "VENNset"): extracts data from vennset slot

Author

Thomas Girke

See also

overLapper, vennPlot, olBarplot, INTERSECTset-class

Examples

showClass("VENNset")
#> Class "VENNset" [package "systemPipeR"]
#> 
#> Slots:
#>                                                                           
#> Name:           setlist  intersectmatrix complexitylevels         vennlist
#> Class:             list           matrix          integer             list

## Sample data
setlist <- list(A=sample(letters, 18), B=sample(letters, 16),
                C=sample(letters, 20), D=sample(letters, 22),
                E=sample(letters, 18), F=sample(letters, 22))

## Create VENNset
vennset <- overLapper(setlist[1:5], type="vennsets")
class(vennset)
#> [1] "VENNset"
#> attr(,"package")
#> [1] "systemPipeR"

## Accessor methods for VENNset/INTERSECTset objects
names(vennset)
#> [1] "setlist"          "intersectmatrix"  "complexitylevels" "vennlist"        
setlist(vennset)
#> $A
#>  [1] "y" "j" "h" "n" "i" "u" "x" "v" "r" "l" "p" "g" "s" "d" "o" "f" "k" "c"
#> 
#> $B
#>  [1] "j" "m" "t" "o" "p" "v" "l" "u" "k" "s" "e" "n" "d" "y" "q" "g"
#> 
#> $C
#>  [1] "l" "k" "f" "p" "e" "v" "w" "j" "m" "u" "o" "h" "z" "n" "a" "q" "g" "d" "c"
#> [20] "r"
#> 
#> $D
#>  [1] "l" "a" "q" "b" "m" "e" "y" "k" "s" "g" "o" "t" "d" "z" "h" "v" "w" "p" "n"
#> [20] "r" "j" "i"
#> 
#> $E
#>  [1] "z" "x" "a" "p" "w" "t" "b" "j" "o" "e" "m" "r" "g" "v" "n" "h" "d" "f"
#> 
intersectmatrix(vennset)
#>   A B C D E
#> a 0 0 1 1 1
#> b 0 0 0 1 1
#> c 1 0 1 0 0
#> d 1 1 1 1 1
#> e 0 1 1 1 1
#> f 1 0 1 0 1
#> g 1 1 1 1 1
#> h 1 0 1 1 1
#> i 1 0 0 1 0
#> j 1 1 1 1 1
#> k 1 1 1 1 0
#> l 1 1 1 1 0
#> m 0 1 1 1 1
#> n 1 1 1 1 1
#> o 1 1 1 1 1
#> p 1 1 1 1 1
#> q 0 1 1 1 0
#> r 1 0 1 1 1
#> s 1 1 0 1 0
#> t 0 1 0 1 1
#> u 1 1 1 0 0
#> v 1 1 1 1 1
#> w 0 0 1 1 1
#> x 1 0 0 0 1
#> y 1 1 0 1 0
#> z 0 0 1 1 1
complexitylevels(vennset)
#>  [1] 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 4 4 4 4 4 5
vennlist(vennset)
#> $A
#> character(0)
#> 
#> $B
#> character(0)
#> 
#> $C
#> character(0)
#> 
#> $D
#> character(0)
#> 
#> $E
#> character(0)
#> 
#> $A_B
#> character(0)
#> 
#> $A_C
#> [1] "c"
#> 
#> $A_D
#> [1] "i"
#> 
#> $A_E
#> [1] "x"
#> 
#> $B_C
#> character(0)
#> 
#> $B_D
#> character(0)
#> 
#> $B_E
#> character(0)
#> 
#> $C_D
#> character(0)
#> 
#> $C_E
#> character(0)
#> 
#> $D_E
#> [1] "b"
#> 
#> $A_B_C
#> [1] "u"
#> 
#> $A_B_D
#> [1] "s" "y"
#> 
#> $A_B_E
#> character(0)
#> 
#> $A_C_D
#> character(0)
#> 
#> $A_C_E
#> [1] "f"
#> 
#> $A_D_E
#> character(0)
#> 
#> $B_C_D
#> [1] "q"
#> 
#> $B_C_E
#> character(0)
#> 
#> $B_D_E
#> [1] "t"
#> 
#> $C_D_E
#> [1] "a" "w" "z"
#> 
#> $A_B_C_D
#> [1] "k" "l"
#> 
#> $A_B_C_E
#> character(0)
#> 
#> $A_B_D_E
#> character(0)
#> 
#> $A_C_D_E
#> [1] "h" "r"
#> 
#> $B_C_D_E
#> [1] "e" "m"
#> 
#> $A_B_C_D_E
#> [1] "d" "g" "j" "n" "o" "p" "v"
#> 

## Coerce VENNset/INTERSECTset object to list
as.list(vennset)
#> $setlist
#> $setlist$A
#>  [1] "y" "j" "h" "n" "i" "u" "x" "v" "r" "l" "p" "g" "s" "d" "o" "f" "k" "c"
#> 
#> $setlist$B
#>  [1] "j" "m" "t" "o" "p" "v" "l" "u" "k" "s" "e" "n" "d" "y" "q" "g"
#> 
#> $setlist$C
#>  [1] "l" "k" "f" "p" "e" "v" "w" "j" "m" "u" "o" "h" "z" "n" "a" "q" "g" "d" "c"
#> [20] "r"
#> 
#> $setlist$D
#>  [1] "l" "a" "q" "b" "m" "e" "y" "k" "s" "g" "o" "t" "d" "z" "h" "v" "w" "p" "n"
#> [20] "r" "j" "i"
#> 
#> $setlist$E
#>  [1] "z" "x" "a" "p" "w" "t" "b" "j" "o" "e" "m" "r" "g" "v" "n" "h" "d" "f"
#> 
#> 
#> $intersectmatrix
#>   A B C D E
#> a 0 0 1 1 1
#> b 0 0 0 1 1
#> c 1 0 1 0 0
#> d 1 1 1 1 1
#> e 0 1 1 1 1
#> f 1 0 1 0 1
#> g 1 1 1 1 1
#> h 1 0 1 1 1
#> i 1 0 0 1 0
#> j 1 1 1 1 1
#> k 1 1 1 1 0
#> l 1 1 1 1 0
#> m 0 1 1 1 1
#> n 1 1 1 1 1
#> o 1 1 1 1 1
#> p 1 1 1 1 1
#> q 0 1 1 1 0
#> r 1 0 1 1 1
#> s 1 1 0 1 0
#> t 0 1 0 1 1
#> u 1 1 1 0 0
#> v 1 1 1 1 1
#> w 0 0 1 1 1
#> x 1 0 0 0 1
#> y 1 1 0 1 0
#> z 0 0 1 1 1
#> 
#> $complexitylevels
#>  [1] 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 4 4 4 4 4 5
#> 
#> $vennlist
#> $vennlist$A
#> character(0)
#> 
#> $vennlist$B
#> character(0)
#> 
#> $vennlist$C
#> character(0)
#> 
#> $vennlist$D
#> character(0)
#> 
#> $vennlist$E
#> character(0)
#> 
#> $vennlist$A_B
#> character(0)
#> 
#> $vennlist$A_C
#> [1] "c"
#> 
#> $vennlist$A_D
#> [1] "i"
#> 
#> $vennlist$A_E
#> [1] "x"
#> 
#> $vennlist$B_C
#> character(0)
#> 
#> $vennlist$B_D
#> character(0)
#> 
#> $vennlist$B_E
#> character(0)
#> 
#> $vennlist$C_D
#> character(0)
#> 
#> $vennlist$C_E
#> character(0)
#> 
#> $vennlist$D_E
#> [1] "b"
#> 
#> $vennlist$A_B_C
#> [1] "u"
#> 
#> $vennlist$A_B_D
#> [1] "s" "y"
#> 
#> $vennlist$A_B_E
#> character(0)
#> 
#> $vennlist$A_C_D
#> character(0)
#> 
#> $vennlist$A_C_E
#> [1] "f"
#> 
#> $vennlist$A_D_E
#> character(0)
#> 
#> $vennlist$B_C_D
#> [1] "q"
#> 
#> $vennlist$B_C_E
#> character(0)
#> 
#> $vennlist$B_D_E
#> [1] "t"
#> 
#> $vennlist$C_D_E
#> [1] "a" "w" "z"
#> 
#> $vennlist$A_B_C_D
#> [1] "k" "l"
#> 
#> $vennlist$A_B_C_E
#> character(0)
#> 
#> $vennlist$A_B_D_E
#> character(0)
#> 
#> $vennlist$A_C_D_E
#> [1] "h" "r"
#> 
#> $vennlist$B_C_D_E
#> [1] "e" "m"
#> 
#> $vennlist$A_B_C_D_E
#> [1] "d" "g" "j" "n" "o" "p" "v"
#> 
#>