circos plot in R

FIN=read.table(IN,header=TRUE)

circos.clear()

circos.par("start.degree" = 90)

circos.initialize("chrB", xlim = c(0, 171823))

circos.track(ylim = c(0, 1), bg.border = "white")

for (i in 1:nrow(FIN)){

  COL1<- scales::alpha(ifelse(FIN[i,]$lib=="a","#4CAF50",ifelse(FIN[i,]$lib=="b","#FF6A6A","#00FA9A")),alpha=ifelse(FIN[i,]$lib=="a",0.8,ifelse(FIN[i,]$lib=="b",0.4,0.0)))

  WID1<-ifelse(FIN[i,]$lib=="a",FIN[i,]$petnum/9,ifelse(FIN[i,]$lib=="b",FIN[i,]$petnum/10,FIN[i,]$petnum/10))

  mid1<-FIN[i,]$start1+(FIN[i,]$end1-FIN[i,]$start1)/2

  mid2<-FIN[i,]$start2+(FIN[i,]$end2-FIN[i,]$start2)/2

  circos.link(FIN[i,]$chr1,mid1,FIN[i,]$chr2,mid2,lwd=WID1,col=COL1)}

library(ggbio)

N <- 100

library(GenomicRanges)

## ======================================================================

##  simmulated GRanges

## ======================================================================

gr <- GRanges(seqnames =

                sample(c("chr1", "chr2", "chr3"),

                       size = N, replace = TRUE),

              IRanges(

                start = sample(1:300, size = N, replace = TRUE),

                width = sample(70:75, size = N,replace = TRUE)),

              strand = sample(c("+", "-", "*"), size = N,

                              replace = TRUE),

              value = rnorm(N, 10, 3), score = rnorm(N, 100, 30),

              sample = sample(c("Normal", "Tumor"),

                              size = N, replace = TRUE),

              pair = sample(letters, size = N,

                            replace = TRUE))

seqlengths(gr) <- c(400, 500, 700)

values(gr)$to.gr <- gr[sample(1:length(gr), size = length(gr))]

## doesn't pass gr to the ggplot

ggplot() + layout_circle(gr, geom = "ideo", fill = "gray70", radius = 7, trackWidth = 3) +

  layout_circle(gr, geom = "bar", radius = 10, trackWidth = 4, aes(fill = score, y = score)) +

  layout_circle(gr, geom = "point", color = "red", radius = 14,

                trackWidth = 3, grid = TRUE, aes(y = score)) +

  layout_circle(gr, geom = "link", linked.to = "to.gr", radius = 6,

                trackWidth = 1)

library(ggplot2)

ggplot(SIN,aes(start,score1))+

   geom_line()+

  geom_rect(xmin=0,xmax=max(SIN$score1),ymin=-100000,ymax=0,fill="red")+

  coord_polar()

library(gcookbook)  # Load gcookbook for the wind data set

ggplot(wind, aes(x = DirCat, fill = SpeedCat)) +

  geom_histogram(binwidth = 15, boundary = -7.5) +

  coord_polar() +

  scale_x_continuous(limits = c(0,360))

circos plot in R的相关教程结束。