http://112.125.26.206:3001/alluvial-diagram/
现在许多文章都利用桑基图来展示ceRNA网络、功能富集等图，也有很多R包专门可以用来画桑基图，不过小编在这里发现ggplot2包非常强大，也可以画桑基图，现在来给大家介绍一下
首先加载需要的R包
###########加载
library(ggplot2)
library(ggalluvial)
library(RColorBrewer)
这里以miRNA-mRNA的关系为例，数据格式如下
##########整合
miRNA_mRNA$Freq=1#定义纵坐标，一般默认为1
miRNA_mRNA_long<- to_lodes_form(miRNA_mRNA,
axes = 1:2,#将miRNA和mRNA分别编号
id = "Cohort") #改为长数据便于画图
下面就可以开始画桑基图了，主要需要ggplot的geom_flow和geom_stratum两个函数
geom_flow--画流动图
我们看一下只画geom_flow的效果
###########geom_flow
ggplot(miRNA_mRNA_long,
aes(x =factor(x,level = c("miRNA","SYMBOL")),y=Freq,stratum = stratum, alluvium = Cohort,fill = stratum, label =stratum)) +
geom_flow( width = 1/3)+#画流动图
geom_text(stat ="stratum" , size =3) +#添加名字
scale_x_discrete(limits = c() )+#去掉横坐标轴
theme_bw()+#定义主题
theme(legend.position = "none",
axis.title = element_blank(),
axis.text.y= element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank())+
scale_fill_manual(values = colorRampPalette(brewer.pal(8, "Accent"))(20))#定义颜色
geom_flow--画流动图
我们看一下只画geom_stratum的效果
###########geom_stratum
ggplot(miRNA_mRNA_long,
aes(x =factor(x,level = c("miRNA","SYMBOL")),y=Freq,stratum = stratum, alluvium = Cohort,fill = stratum, label =stratum)) +
geom_stratum( width = 1/3,linetype=1,size=0.5,alpha =0.5,color = "black") +#画冲击图
geom_text(stat ="stratum" , size =3) +#添加名字
scale_x_discrete(limits = c() )+#去掉横坐标轴
theme_bw()+#定义主题
theme(legend.position = "none",
axis.title = element_blank(),
axis.text.y= element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank())+
scale_fill_manual(values = colorRampPalette(brewer.pal(8, "Accent"))(20))#定义颜色
整合后
###########绘图
ggplot(miRNA_mRNA_long,
aes(x =factor(x,level = c("miRNA","SYMBOL")),y=Freq,stratum = stratum, alluvium = Cohort,fill = stratum, label =stratum)) +
geom_flow( width = 1/3)+#画流动图
geom_stratum( width = 1/3,linetype=1,size=0.5,alpha =0.5,color = "black") +#画冲击图
geom_text(stat ="stratum" , size =3) +#添加名字
scale_x_discrete(limits = c() )+#去掉横坐标轴
theme_bw()+#定义主题
theme(legend.position = "none",
axis.title = element_blank(),
axis.text.y= element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank())+#去掉边界线
scale_fill_manual(values = colorRampPalette(brewer.pal(8, "Accent"))(20))#定义颜色
改变边框模式linetype
###########绘图
ggplot(miRNA_mRNA_long,
aes(x =factor(x,level = c("miRNA","SYMBOL")),y=Freq,stratum = stratum, alluvium = Cohort,fill = stratum, label =stratum)) +
geom_flow( width = 1/3)+#画流动图
geom_stratum( width = 1/3,linetype=0,size=0.5,alpha =0.5,color = "black") +#画冲击图
geom_text(stat ="stratum" , size =3) +#添加名字
scale_x_discrete(limits = c() )+#去掉横坐标轴
theme_bw()+#定义主题
theme(legend.position = "none",
axis.title = element_blank(),
axis.text.y= element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank())+#去掉边界线
scale_fill_manual(values = colorRampPalette(brewer.pal(8, "Accent"))(20))#定义颜色
