R语言基础绘图教程——第6章:箱形图和韦恩图

dat <- read.table("boxplot.txt",header=T)
boxplot(Value~Group,data = dat)

#调整
boxplot(Value~Group,data = dat,
        varwidth=TRUE,
        col="#6DC9F2",
        outline=FALSE,
        names=c("Control","Drug1","Drug2","Drug3","Drug4","Drug5"),
        horizontal=FALSE )

#高级调整
points(jitter(as.numeric(dat$Group)),dat$Value, pch = 16, col = "red")

ggplot(dat, aes(Group,Value))+ geom_boxplot()

####first generate the test data
#a function to generate gene names
generateGeneName <- function()
{
  paste(sample(LETTERS,5,replace=T), collapse='')
}

#generate 100 gene names
geneNames <- replicate(1000, generateGeneName())


####method 1
####
library(gplots)
#venn plot of two groups 
GroupA <- sample(geneNames,400, replace=F)
GroupB <- sample(geneNames,400, replace=F)
input <- list(GroupA,GroupB)
venn(input)

#venn plot of three groups 
GroupA <- sample(geneNames,400, replace=F)
GroupB <- sample(geneNames,400, replace=F)
GroupC <- sample(geneNames,500, replace=F)
input <- list(GroupA,GroupB,GroupC)
venn(input)

#venn plot of four groups 
GroupA <- sample(geneNames,400, replace=F)
GroupB <- sample(geneNames,300, replace=F)
GroupC <- sample(geneNames,500, replace=F)
GroupD <- sample(geneNames,700, replace=F)
input <- list(GroupA,GroupB,GroupC,GroupD)
venn(input)

#venn plot of five groups 
GroupA <- sample(geneNames,400, replace=F)
GroupB <- sample(geneNames,300, replace=F)
GroupC <- sample(geneNames,500, replace=F)
GroupD <- sample(geneNames,700, replace=F)
GroupE <- sample(geneNames,600, replace=F)
input <- list(GroupA,GroupB,GroupC,GroupD,GroupE)
venn(input)

####method2
####using package "venneuler", with weights. using the size of the area to indicate different sets and the intersection
library(venneuler)
m <- data.frame(c(GroupA, GroupB, GroupC), 
               c(rep("GroupA", length(GroupA)),
                 rep("GroupB", length(GroupB)),
                 rep("GroupC", length(GroupC))
                )
              )
v <- venneuler(m)
plot(v)

####method3
####
library(VennDiagram)
#three groups
venn.diagram(list(GroupA=sample(geneNames,400, replace=F),
                  GroupB=sample(geneNames,300, replace=F),
                  GroupC=sample(geneNames,500, replace=F) ),
             height=3000,
             width=3000,
             resolution=500,
             imagetype="tiff",
             filename="venn.diagram.3groups.tiff",
             fill = c("cornflowerblue", "green", "yellow"),
             label.col="black",
             cat.col = c("darkblue", "darkgreen", "orange")
)
#four groups
venn.diagram(list(GroupA=sample(geneNames,400, replace=F),
                  GroupB=sample(geneNames,300, replace=F),
                  GroupC=sample(geneNames,500, replace=F),
                  GroupD=sample(geneNames,700, replace=F) ),
             height=3000,
             width=3000,
             resolution=500,
             imagetype="tiff",
             filename="venn.diagram.4groups.tiff",
             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")
)
#five groups
venn.diagram(list(GroupA=sample(geneNames,400, replace=F),
                  GroupB=sample(geneNames,300, replace=F),
                  GroupC=sample(geneNames,500, replace=F),
                  GroupD=sample(geneNames,700, replace=F),
                  GroupE=sample(geneNames,800, replace=F)),
             height=3000,
             width=3000,
             resolution=500,
             imagetype="tiff",
             filename="venn.diagram.5groups.tiff",
             col = "black",
             fill = c("dodgerblue", "goldenrod1", "darkorange1", "seagreen3", "orchid3"),
             alpha = 0.50,
             cex = c(1.5, 1.5, 1.5, 1.5, 1.5, 1, 0.8, 1, 0.8, 1, 0.8, 1, 0.8,
                     1, 0.8, 1, 0.55, 1, 0.55, 1, 0.55, 1, 0.55, 1, 0.55, 1, 1, 1, 1, 1, 1.5),
             cat.col = c("dodgerblue", "goldenrod1", "darkorange1", "seagreen3", "orchid3"),
             cat.cex = 1.5,
             cat.fontface = "bold",
             margin = 0.1
)