Windows系统下R语言环境搭建及高级图表绘制

1、R语言环境及其编译软件下载安装：

链接：https://pan.baidu.com/s/186hjytYEqJB2kDUed0beAA 
提取码：mtwh

先安装R-4.0.3-win.exe，这个是提供R语言环境，安装完成后，桌面上会出现如下图标：

打开运行

再安装RStudio-1.3.1093.exe，这个是编译R语言的软件，安装完成后将rstudio.exe发送到桌面运行。

2、画箱线图

h<-c(144,166,163,143,152,169,130,159,160,175,161,170, 146,159,150,183,165,146,169)

boxplot(h)

 

3、画桑基图

install.packages("data.table") 
library(data.table)
install.packages("pillar")
library("pillar")
install.packages("highcharter")
library("highcharter")

sankey_data<-data.table(from = c("巴西",    "巴西",   "巴西",   "巴西",   "加拿大",  "加拿大",  "加拿大",  "墨西哥",  "墨西哥",  "墨西哥",  "墨西哥",  "美国",   "美国",   "美国",   "美国",   "葡萄牙",  "葡萄牙",  "葡萄牙",  "葡萄牙",  "法国",   "法国",   "法国",   "法国",   "法国",   "西班牙",  "西班牙",  "西班牙",  "英国",   "英国",   "英国",   "英国",   "南非",   "南非",   "南非",   "安哥拉",  "安哥拉",  "安哥拉",  "塞内加尔", "塞内加尔", "塞内加尔", "马里",   "马里",   "马里",   "摩洛哥",  "摩洛哥",  "摩洛哥"),
                          to = c("葡萄牙",    "法国",   "西班牙",  "英国",   "葡萄牙",  "法国",   "英国",   "葡萄牙",  "法国",   "西班牙",  "英国",   "葡萄牙",  "法国",   "西班牙",  "英国",   "安哥拉",  "塞内加尔", "摩洛哥",  "南非",   "安哥拉",  "塞内加尔", "马里",   "摩洛哥",  "南非",   "塞内加尔", "摩洛哥",  "南非",   "安哥拉",  "塞内加尔", "摩洛哥",  "南非",   "中国",   "印度",   "日本",   "中国",   "印度",   "日本",   "中国",   "印度",   "日本",   "中国",   "印度",   "日本",   "中国",   "印度",   "日本"),
                          weight = c(5,    1,  1,  1,  1,  5,  1,  1,  1,  5,  1,  1,  1,  1,  5,  2,  1,  1,  3,  1,  3,  3,  3,  1,  1,  3,  1,  1,  1,  2,  7,  5,  1,  3,  5,  1,  3,  5,  1,  3,  5,  1,  3,  5,  1,  3))

highchart() %>%
  hc_title(text = "桑基图") %>%
  hc_add_series(data = sankey_data,type = "sankey",hcaes(from = from,to = to,weight = weight)) %>%
  hc_add_theme(hc_theme_google())

4、Chord图

getwd()
setwd(getwd())
library(circlize)
library(Cairo)
library(usethis)
library(devtools)

bed1 = generateRandomBed(nr = 100)
bed1 = bed1[sample(nrow(bed1), 20), ]
bed2 = generateRandomBed(nr = 100)
bed2 = bed2[sample(nrow(bed2), 20), ]

cairo_pdf('Chord.pdf',width = 8,height = 8,pointsize = 10)
circos.par("track.height" = 0.1, cell.padding = c(0, 0, 0, 0))
circos.initializeWithIdeogram()
circos.genomicLink(bed1, bed2, col = sample(1:5, 20, replace = TRUE), border = NA)
circos.clear()
dev.off()

5、Circos图

library(RCircos)
library(Cairo)
data(UCSC.HG19.Human.CytoBandIdeogram)
head(UCSC.HG19.Human.CytoBandIdeogram)

###########
#chr.exclude<-NULL #设置不显示的染色体，如 c(1,3)
#tracks.inside <-10 #设置内部track 个数
#tracks.outside<-0 #设置外部track 个数
RCircos.Set.Core.Components(cyto.info=UCSC.HG19.Human.CytoBandIdeogram,chr.exclude=NULL,tracks.inside=5,tracks.outside=0)

outF<-'Circos.pdf'
cairo_pdf(outF,width = 8,height = 8)
RCircos.Set.Plot.Area()
RCircos.Chromosome.Ideogram.Plot()

data(RCircos.Scatter.Data)
RCircos.Scatter.Plot(RCircos.Scatter.Data, data.col=5,track.num=1, side='in', by.fold=1)

data(RCircos.Histogram.Data)
RCircos.Histogram.Plot(RCircos.Histogram.Data,data.col = 4,track.num = 3,side = 'in')

data(RCircos.Link.Data)
RCircos.Link.Plot(RCircos.Link.Data,track.num=4,TRUE)

data(RCircos.Ribbon.Data)
RCircos.Ribbon.Plot(ribbon.data=RCircos.Ribbon.Data, track.num=5, by.chromosome=FALSE, twist=FALSE)
dev.off()