library(ggplot2)
library(hrbrthemes)
library(corrplot)

data <- read.csv("fig2_section2_batch1_rpm.csv", header = TRUE,sep=',',encoding="utf-8",stringsAsFactors=F)
matrix2=cor(data[2:25])

jpeg(file="fig_a.jpg", width=5, height=5, units="in", res=500)
corrplot(corr=matrix2,method = "color",tl.col="black",tl.cex=0.9,cl.pos="n",order = "AOE")
dev.off()

library(ggplot2)
library(hrbrthemes)
library(corrplot)

data2 <- read.csv("suppl_fig2a_logRPM_batch2.csv", header = TRUE,sep=',',encoding="utf-8",stringsAsFactors=F)
matrix=cor(data2[2:11])

jpeg(file="fig_b.jpg", width=5, height=5, units="in", res=800)
corrplot(corr=matrix,method = "color",tl.col="black",addCoef.col = "white",number.cex = 0.8,order = "AOE",tl.cex=1.2,cl.pos="n")
dev.off()

library(ggplot2)
library(hrbrthemes)
library(ggpubr)

data <- read.csv("clusterData_rpm.csv", header = TRUE,sep=',',encoding="utf-8",stringsAsFactors=F)

#fig1
pic1=ggplot(data, aes(x=intron0_1, y=intron0_2))+
	geom_point(
		color=rgb(0.4,0.4,0.8,0.6),
		shape=19,
		alpha=0.8,
		size=2.5
	) +
	stat_cor(data=data,aes(label = ..r.label..), method = "spearman",cex=6)+
	theme_bw() +
	stat_smooth(method = 'lm',color="red",lwd=0.6)+
	scale_x_continuous(labels = scales::comma)+
	scale_y_continuous(labels = scales::comma)+
	theme(axis.line=element_line(size=0.5,colour="black"),panel.grid=element_blank())+
	theme(plot.margin=unit(rep(1,4),'lines'))+
	theme(axis.text.y=element_text(size=18),
		axis.text.x = element_text(size=18,vjust = 0.5, hjust = 0.5, angle = 35),
		axis.title.y=element_text(size=20,vjust = 2),
		axis.title.x = element_text(size=20,vjust = 0.5),
		panel.grid.minor.x=element_blank(),
		panel.grid.minor.y=element_blank())

jpeg(file="fig_c1.jpg", width=5, height=5, units="in", res=800)
pic1
dev.off()

#fig2
pic1=ggplot(data, aes(x=intron0_1, y=intron0_3))+
	geom_point(
		color=rgb(0.4,0.4,0.8,0.6),
		shape=19,
		alpha=0.8,
		size=2.5
	) +
	stat_cor(data=data,aes(label = ..r.label..), method = "spearman",cex=6)+
	theme_bw() +
	stat_smooth(method = 'lm',color="red",lwd=0.6)+
	scale_x_continuous(labels = scales::comma)+
	scale_y_continuous(labels = scales::comma)+
	theme(axis.line=element_line(size=0.5,colour="black"),panel.grid=element_blank())+
	theme(plot.margin=unit(rep(1,4),'lines'))+
	theme(axis.text.y=element_text(size=18),
		axis.text.x = element_text(size=18,vjust = 0.5, hjust = 0.5, angle = 35),
		axis.title.y=element_text(size=20,vjust = 2),
		axis.title.x = element_text(size=20,vjust = 0.5),
		panel.grid.minor.x=element_blank(),
		panel.grid.minor.y=element_blank())

jpeg(file="fig_c2.jpg", width=5, height=5, units="in", res=800)
pic1
dev.off()

#fig3
pic1=ggplot(data, aes(x=intron0_2, y=intron0_3))+
	geom_point(
		color=rgb(0.4,0.4,0.8,0.6),
		shape=19,
		alpha=0.8,
		size=2.5
	) +
	stat_cor(data=data,aes(label = ..r.label..), method = "spearman",cex=6)+
	theme_bw() +
	stat_smooth(method = 'lm',color="red",lwd=0.6)+
	scale_x_continuous(labels = scales::comma)+
	scale_y_continuous(labels = scales::comma)+
	theme(axis.line=element_line(size=0.5,colour="black"),panel.grid=element_blank())+
	theme(plot.margin=unit(rep(1,4),'lines'))+
	theme(axis.text.y=element_text(size=18),
		axis.text.x = element_text(size=18,vjust = 0.5, hjust = 0.5, angle = 35),
		axis.title.y=element_text(size=20,vjust = 2),
		axis.title.x = element_text(size=20,vjust = 0.5),
		panel.grid.minor.x=element_blank(),
		panel.grid.minor.y=element_blank())

jpeg(file="fig_c3.jpg", width=5, height=5, units="in", res=800)
pic1
dev.off()

#fig4
pic2=ggplot(data, aes(x=intron2_1, y=intron2_2))+
	geom_point(
		color=rgb(0.4,0.4,0.8,0.6),
		shape=19,
		alpha=0.8,
		size=2.5
	) +
	stat_cor(data=data,aes(label = ..r.label..), method = "spearman",cex=6)+
	theme_bw() +
	stat_smooth(method = 'lm',color="red",lwd=0.6)+
	scale_x_continuous(labels = scales::comma)+
	scale_y_continuous(labels = scales::comma)+
	theme(axis.line=element_line(size=0.5,colour="black"),panel.grid=element_blank())+
	theme(plot.margin=unit(rep(1,4),'lines'))+
	theme(axis.text.y=element_text(size=18),
		axis.text.x = element_text(size=18,vjust = 0.5, hjust = 0.5, angle = 35),
		axis.title.y=element_text(size=20,vjust = 2),
		axis.title.x = element_text(size=20,vjust = 0.5),
		panel.grid.minor.x=element_blank(),
		panel.grid.minor.y=element_blank())

jpeg(file="fig_c4.jpg", width=5, height=5, units="in", res=800)
pic2
dev.off()

#fig5
pic2=ggplot(data, aes(x=intron2_1, y=intron2_3))+
	geom_point(
		color=rgb(0.4,0.4,0.8,0.6),
		shape=19,
		alpha=0.8,
		size=2.5
	) +
	stat_cor(data=data,aes(label = ..r.label..), method = "spearman",cex=6,label.x = 0, label.y = 35000)+
	theme_bw() +
	stat_smooth(method = 'lm',color="red",lwd=0.6)+
	scale_x_continuous(labels = scales::comma)+
	scale_y_continuous(labels = scales::comma)+
	theme(axis.line=element_line(size=0.5,colour="black"),panel.grid=element_blank())+
	theme(plot.margin=unit(rep(1,4),'lines'))+
	theme(axis.text.y=element_text(size=18),
		axis.text.x = element_text(size=18,vjust = 0.5, hjust = 0.5, angle = 35),
		axis.title.y=element_text(size=20,vjust = 2),
		axis.title.x = element_text(size=20,vjust = 0.5),
		panel.grid.minor.x=element_blank(),
		panel.grid.minor.y=element_blank())

jpeg(file="fig_c5.jpg", width=5, height=5, units="in", res=800)
pic2
dev.off()

#fig6
pic2=ggplot(data, aes(x=intron2_2, y=intron2_3))+
	geom_point(
		color=rgb(0.4,0.4,0.8,0.6),
		shape=19,
		alpha=0.8,
		size=2.5
	) +
	stat_cor(data=data,aes(label = ..r.label..), method = "spearman",cex=6,label.x = 0, label.y = 32000)+
	theme_bw() +
	stat_smooth(method = 'lm',color="red",lwd=0.6)+
	scale_x_continuous(labels = scales::comma)+
	scale_y_continuous(labels = scales::comma)+
	theme(axis.line=element_line(size=0.5,colour="black"),panel.grid=element_blank())+
	theme(plot.margin=unit(rep(1,4),'lines'))+
	theme(axis.text.y=element_text(size=18),
		axis.text.x = element_text(size=18,vjust = 0.5, hjust = 0.5, angle = 35),
		axis.title.y=element_text(size=20,vjust = 2),
		axis.title.x = element_text(size=20,vjust = 0.5),
		panel.grid.minor.x=element_blank(),
		panel.grid.minor.y=element_blank())

jpeg(file="fig_c6.jpg", width=5, height=5, units="in", res=800)
pic2
dev.off()

#fig7
pic3=ggplot(data, aes(x=intron6_1, y=intron6_2))+
	geom_point(
		color=rgb(0.4,0.4,0.8,0.6),
		shape=19,
		alpha=0.8,
		size=2.5
	) +
	stat_cor(data=data, aes(label = ..r.label..),method = "spearman",cex=6)+
	theme_bw() +
	stat_smooth(method = 'lm',color="red",lwd=0.6)+
	scale_x_continuous(labels = scales::comma)+
	scale_y_continuous(labels = scales::comma)+
	theme(axis.line=element_line(size=0.5,colour="black"),panel.grid=element_blank())+
	theme(plot.margin = unit(c(1, 2, 1, 1), "lines"))+
	theme(axis.text.y=element_text(size=18),
		axis.text.x = element_text(size=18,vjust = 0.5, hjust = 0.5, angle = 35),
		axis.title.y=element_text(size=20,vjust = 2),
		axis.title.x = element_text(size=20,vjust = 0.5),
		panel.grid.minor.x=element_blank(),
		panel.grid.minor.y=element_blank())

jpeg(file="fig_c7.jpg", width=5.1, height=5, units="in", res=800)
pic3
dev.off()

#fig8
pic3=ggplot(data, aes(x=intron6_1, y=intron6_3))+
	geom_point(
		color=rgb(0.4,0.4,0.8,0.6),
		shape=19,
		alpha=0.8,
		size=2.5
	) +
	stat_cor(data=data, aes(label = ..r.label..),method = "spearman",cex=6)+
	theme_bw() +
	stat_smooth(method = 'lm',color="red",lwd=0.6)+
	scale_x_continuous(labels = scales::comma)+
	scale_y_continuous(labels = scales::comma)+
	theme(axis.line=element_line(size=0.5,colour="black"),panel.grid=element_blank())+
	theme(plot.margin = unit(c(1, 2, 1, 1), "lines"))+
	theme(axis.text.y=element_text(size=18),
		axis.text.x = element_text(size=18,vjust = 0.5, hjust = 0.5, angle = 35),
		axis.title.y=element_text(size=20,vjust = 2),
		axis.title.x = element_text(size=20,vjust = 0.5),
		panel.grid.minor.x=element_blank(),
		panel.grid.minor.y=element_blank())

jpeg(file="fig_c8.jpg", width=5.1, height=5, units="in", res=800)
pic3
dev.off()

#fig9
pic3=ggplot(data, aes(x=intron6_2, y=intron6_3))+
	geom_point(
		color=rgb(0.4,0.4,0.8,0.6),
		shape=19,
		alpha=0.8,
		size=2.5
	) +
	stat_cor(data=data, aes(label = ..r.label..),method = "spearman",cex=6)+
	theme_bw() +
	stat_smooth(method = 'lm',color="red",lwd=0.6)+
	scale_x_continuous(labels = scales::comma)+
	scale_y_continuous(labels = scales::comma)+
	theme(axis.line=element_line(size=0.5,colour="black"),panel.grid=element_blank())+
	theme(plot.margin = unit(c(1, 2, 1, 1), "lines"))+
	theme(axis.text.y=element_text(size=18),
		axis.text.x = element_text(size=18,vjust = 0.5, hjust = 0.5, angle = 35),
		axis.title.y=element_text(size=20,vjust = 2),
		axis.title.x = element_text(size=20,vjust = 0.5),
		panel.grid.minor.x=element_blank(),
		panel.grid.minor.y=element_blank())

jpeg(file="fig_c9.jpg", width=5.1, height=5, units="in", res=800)
pic3
dev.off()

#fig10
pic4=ggplot(data, aes(x=intron12_1, y=intron12_2))+
	geom_point(
		color=rgb(0.4,0.4,0.8,0.6),
		shape=19,
		alpha=0.8,
		size=2.5
	) +
	stat_cor(data=data,aes(label = ..r.label..), method = "spearman",cex=6,label.x = 0,label.y =43000)+
	theme_bw() +
	stat_smooth(method = 'lm',color="red",lwd=0.6)+
	scale_x_continuous(labels = scales::comma)+
	scale_y_continuous(labels = scales::comma)+
	theme(axis.line=element_line(size=0.5,colour="black"),panel.grid=element_blank())+
	theme(plot.margin=unit(rep(1,4),'lines'))+
	theme(axis.text.y=element_text(size=18),
		axis.text.x = element_text(size=18,vjust = 0.5, hjust = 0.5, angle = 35),
		axis.title.y=element_text(size=20,vjust = 2),
		axis.title.x = element_text(size=20,vjust = 0.5),
		panel.grid.minor.x=element_blank(),
		panel.grid.minor.y=element_blank())

jpeg(file="fig_c10.jpg", width=5, height=5, units="in", res=800)
pic4
dev.off()

#fig11
pic4=ggplot(data, aes(x=intron12_1, y=intron12_3))+
	geom_point(
		color=rgb(0.4,0.4,0.8,0.6),
		shape=19,
		alpha=0.8,
		size=2.5
	) +
	stat_cor(data=data,aes(label = ..r.label..), method = "spearman",cex=6)+
	theme_bw() +
	stat_smooth(method = 'lm',color="red",lwd=0.6)+
	scale_x_continuous(labels = scales::comma)+
	scale_y_continuous(labels = scales::comma)+
	theme(axis.line=element_line(size=0.5,colour="black"),panel.grid=element_blank())+
	theme(plot.margin=unit(rep(1,4),'lines'))+
	theme(axis.text.y=element_text(size=18),
		axis.text.x = element_text(size=18,vjust = 0.5, hjust = 0.5, angle = 35),
		axis.title.y=element_text(size=20,vjust = 2),
		axis.title.x = element_text(size=20,vjust = 0.5),
		panel.grid.minor.x=element_blank(),
		panel.grid.minor.y=element_blank())

jpeg(file="fig_c11.jpg", width=5, height=5, units="in", res=800)
pic4
dev.off()

#fig12
pic4=ggplot(data, aes(x=intron12_2, y=intron12_3))+
	geom_point(
		color=rgb(0.4,0.4,0.8,0.6),
		shape=19,
		alpha=0.8,
		size=2.5
	) +
	stat_cor(data=data,aes(label = ..r.label..), method = "spearman",cex=6)+
	theme_bw() +
	stat_smooth(method = 'lm',color="red",lwd=0.6)+
	scale_x_continuous(labels = scales::comma)+
	scale_y_continuous(labels = scales::comma)+
	theme(axis.line=element_line(size=0.5,colour="black"),panel.grid=element_blank())+
	theme(plot.margin=unit(rep(1,4),'lines'))+
	theme(axis.text.y=element_text(size=18),
		axis.text.x = element_text(size=18,vjust = 0.5, hjust = 0.5, angle = 35),
		axis.title.y=element_text(size=20,vjust = 2),
		axis.title.x = element_text(size=20,vjust = 0.5),
		panel.grid.minor.x=element_blank(),
		panel.grid.minor.y=element_blank())

jpeg(file="fig_c12.jpg", width=5, height=5, units="in", res=800)
pic4
dev.off()