R绘图基础（五）文氏图vennDiagram 6

> source("http://bioconductor.org/biocLite.R")
> biocLite("limma")
> library(limma)
> hsb2<-read.table("http://www.ats.ucla.edu/stat/R/notes/hsb2.csv", sep=',', header=T)
> attach(hsb2)
> hw<-(write>=60)
> hm<-(math >=60)
> hr<-(read >=60)
> c3<-cbind(hw, hm, hr)
> a <- vennCounts(c3); a
     hw hm hr Counts
[1,]  0  0  0    113
[2,]  0  0  1     18
[3,]  0  1  0      8
[4,]  0  1  1      8
[5,]  1  0  0     12
[6,]  1  0  1      8
[7,]  1  1  0     11
[8,]  1  1  1     22
attr(,"class")
[1] "VennCounts"
> vennDiagram(a, include = "both", names = c("High Writing", "High Math", "High Reading"), cex = 1, counts.col = "red")

> source("http://bioconductor.org/biocLite.R") > biocLite("limma") > library(limma) > hsb2<-read.table("http://www.ats.ucla.edu/stat/R/notes/hsb2.csv", sep=',', header=T) > attach(hsb2) > hw<-(write>=60) > hm<-(math >=60) > hr<-(read >=60) > c3<-cbind(hw, hm, hr) > a <- vennCounts(c3); a hw hm hr Counts [1,] 0 0 0 113 [2,] 0 0 1 18 [3,] 0 1 0 8 [4,] 0 1 1 8 [5,] 1 0 0 12 [6,] 1 0 1 8 [7,] 1 1 0 11 [8,] 1 1 1 22 attr(,"class") [1] "VennCounts" > vennDiagram(a, include = "both", names = c("High Writing", "High Math", "High Reading"), cex = 1, counts.col = "red")

> library(gplots)
> ##
> ## Example using a list of item names belonging to the
> ## specified group.
> ##
> 
> ## construct some fake gene names..
> oneName <- function() paste(sample(LETTERS,5,replace=TRUE),collapse="")
> geneNames <- replicate(1000, oneName())
>                        
> ## 
> GroupA <- sample(geneNames, 400, replace=FALSE)
> GroupB <- sample(geneNames, 750, replace=FALSE)
> GroupC <- sample(geneNames, 250, replace=FALSE)
> GroupD <- sample(geneNames, 300, replace=FALSE)
> input  <-list(GroupA,GroupB,GroupC,GroupD)
> venn(input)

> library(gplots) > ## > ## Example using a list of item names belonging to the > ## specified group. > ## > > ## construct some fake gene names.. > oneName <- function() paste(sample(LETTERS,5,replace=TRUE),collapse="") > geneNames <- replicate(1000, oneName()) > > ## > GroupA <- sample(geneNames, 400, replace=FALSE) > GroupB <- sample(geneNames, 750, replace=FALSE) > GroupC <- sample(geneNames, 250, replace=FALSE) > GroupD <- sample(geneNames, 300, replace=FALSE) > input <-list(GroupA,GroupB,GroupC,GroupD) > venn(input)

> ##
> ## Example using a list of item indexes belonging to the
> ## specified group.
> ##
> GroupA.i <- which(geneNames %in% GroupA)
> GroupB.i <- which(geneNames %in% GroupB)
> GroupC.i <- which(geneNames %in% GroupC)
> GroupD.i <- which(geneNames %in% GroupD)
> input.i  <-list(A=GroupA.i,B=GroupB.i,C=GroupC.i,D=GroupD.i)
> venn(input.i)

> ## > ## Example using a list of item indexes belonging to the > ## specified group. > ## > GroupA.i <- which(geneNames %in% GroupA) > GroupB.i <- which(geneNames %in% GroupB) > GroupC.i <- which(geneNames %in% GroupC) > GroupD.i <- which(geneNames %in% GroupD) > input.i <-list(A=GroupA.i,B=GroupB.i,C=GroupC.i,D=GroupD.i) > venn(input.i)

> ##
> ## Example using a data frame of indicator ('f'lag) columns
> ##
> GroupA.f <- geneNames %in% GroupA
> GroupB.f <- geneNames %in% GroupB
> GroupC.f <- geneNames %in% GroupC
> GroupD.f <- geneNames %in% GroupD
> input.df <- data.frame(A=GroupA.f,B=GroupB.f,C=GroupC.f,D=GroupD.f)
> venn(input.df)

> ## > ## Example using a data frame of indicator ('f'lag) columns > ## > GroupA.f <- geneNames %in% GroupA > GroupB.f <- geneNames %in% GroupB > GroupC.f <- geneNames %in% GroupC > GroupD.f <- geneNames %in% GroupD > input.df <- data.frame(A=GroupA.f,B=GroupB.f,C=GroupC.f,D=GroupD.f) > venn(input.df)

> library("venneuler")
> m <- as.matrix(data.frame(A=c(1.5, 0.2, 0.4, 0, 0),
+                           B=c(0  , 0.2, 0  , 1, 0),
+                           C=c(0  , 0  , 0.3, 0, 1)))
> # without weights
> v <- venneuler(m > 0)
> plot(v)
> # with weights
> v <- venneuler(m)
> plot(v)

> library("venneuler") > m <- as.matrix(data.frame(A=c(1.5, 0.2, 0.4, 0, 0), + B=c(0 , 0.2, 0 , 1, 0), + C=c(0 , 0 , 0.3, 0, 1))) > # without weights > v <- venneuler(m > 0) > plot(v) > # with weights > v <- venneuler(m) > plot(v)

> library(VennDiagram)
> names(input)<-c("A","B","C","D")
> venn.diagram(input,"VennDiagram.venn.png",col = "transparent",fill = c("cornflowerblue", "green", "yellow", "darkorchid1"),alpha = 0.50,label.col = c("orange", "white", "darkorchid4", "white", "white", "white", "white", "white", "darkblue", "white", "white", "white", "white", "darkgreen", "white"),cat.col = c("darkblue", "darkgreen", "orange", "darkorchid4"),)

> library(VennDiagram) > names(input)<-c("A","B","C","D") > venn.diagram(input,"VennDiagram.venn.png",col = "transparent",fill = c("cornflowerblue", "green", "yellow", "darkorchid1"),alpha = 0.50,label.col = c("orange", "white", "darkorchid4", "white", "white", "white", "white", "white", "darkblue", "white", "white", "white", "white", "darkgreen", "white"),cat.col = c("darkblue", "darkgreen", "orange", "darkorchid4"),)