library(dplyr)
library(ggplot2)
library(ggrepel)
BP <- read.table(file ="CC.txt",header = TRUE, sep = "\t")
View(BP)
objects(BP)
BP <- arrange(BP,desc(BP[,2]))
BP$Biological.Processes.Term <- factor(BP$Biological.Processes.Term,levels = rev(BP$Biological.Processes.Term))

p <- ggplot(BP,aes(x=Fold_Enrichment,y=Biological.Processes.Term,
                   colour=p.value,size=Count))+geom_point()+
  scale_size(range=c(2, 8))+
  scale_colour_gradient(low = "blue",high = "red")+
  theme_bw()+
  ylab("Biological.Processes.Term")+
  xlab("Fold Enrichment")+
  labs(color=expression(-log[10](PValue)))+
  theme(legend.title=element_text(size=14), legend.text = element_text(size=14))+
  theme(axis.title.y = element_text(margin = margin(r = 50)),axis.title.x = element_text(margin = margin(t = 20)))+
  theme(axis.text.x = element_text(face ="bold",color="black",angle=0,vjust=1))
p
CC <- read.table(file ="CC.txt",header = TRUE, sep = "\t")
CC <- arrange(CC,desc(CC[,2]))
CC$Cellular.Components.Term <- factor(CC$Cellular.Components.Term,levels = rev(CC$Cellular.Components.Term))
p1 <- ggplot(CC,aes(x=Fold_Enrichment,y=Cellular.Components.Term,
                   colour=p.value,size=Count))+geom_point()+
  scale_size(range=c(2, 8))+
  scale_colour_gradient(low = "blue",high = "red")+
  theme_bw()+
  ylab("Cellular.Components.Term")+
  xlab("Fold Enrichment")+
  labs(color=expression(-log[10](PValue)))+
  theme(legend.title=element_text(size=14), legend.text = element_text(size=14))+
  theme(axis.title.y = element_text(margin = margin(r = 50)),axis.title.x = element_text(margin = margin(t = 20)))+
  theme(axis.text.x = element_text(face ="bold",color="black",angle=0,vjust=1))

MF <- read.table(file ="MF.txt",header = TRUE, sep = "\t")
MF <- arrange(MF,desc(MF[,2]))
MF$Molecular.Function.Term <- factor(MF$Molecular.Function.Term,levels = rev(MF$Molecular.Function.Term))
p2 <- ggplot(MF,aes(x=Fold_Enrichment,y=Molecular.Function.Term,
                   colour=p.value,size=Count))+geom_point()+
  scale_size(range=c(2, 8))+
  scale_colour_gradient(low = "blue",high = "red")+
  theme_bw()+
  ylab("Molecular.Function.Term")+
  xlab("Fold Enrichment")+
  labs(color=expression(-log[10](PValue)))+
  theme(legend.title=element_text(size=14), legend.text = element_text(size=14))+
  theme(axis.title.y = element_text(margin = margin(r = 50)),axis.title.x = element_text(margin = margin(t = 20)))+
  theme(axis.text.x = element_text(face ="bold",color="black",angle=0,vjust=1))

KEGG <- read.table(file ="KEGG.txt",header = TRUE, sep = "\t")
View(KEGG)
objects(KEGG)
KEGG <- arrange(KEGG,desc(KEGG[,2]))
KEGG$KEGG.Pathway.Term <- factor(KEGG$KEGG.Pathway.Term,levels = rev(KEGG$KEGG.Pathway.Term))
p3 <- ggplot(KEGG,aes(x=Fold_Enrichment,y=KEGG.Pathway.Term,
                   colour=p.value,size=Count))+geom_point()+
  scale_size(range=c(2, 8))+
  scale_colour_gradient(low = "blue",high = "red")+
  theme_bw()+
  ylab("KEGG.Pathway.Term")+
  xlab("Fold Enrichment")+
  labs(color=expression(-log[10](PValue)))+
  theme(legend.title=element_text(size=14), legend.text = element_text(size=14))+
  theme(axis.title.y = element_text(margin = margin(r = 50)),axis.title.x = element_text(margin = margin(t = 20)))+
  theme(axis.text.x = element_text(face ="bold",color="black",angle=0,vjust=1))

allgokegg <- read.table(file ="allgokegg.txt",header = TRUE, sep = "\t")
View(allgokegg)
objects(allgokegg)
allgokegg <- arrange(allgokegg,desc(allgokegg[,2]))
allgokegg$all.Term <- factor(allgokegg$all.Term,levels = rev(allgokegg$all.Term))
p4 <- ggplot(allgokegg,aes(x=Fold_Enrichment,y=all.Term,
                   colour=p.value,size=Count))+geom_point()+
  scale_size(range=c(2, 8))+
  scale_colour_gradient(low = "blue",high = "red")+
  theme_bw()+
  ylab("all.Term")+
  xlab("Fold Enrichment")+
  labs(color=expression(-log[10](PValue)))+
  theme(legend.title=element_text(size=14), legend.text = element_text(size=14))+
  theme(axis.title.y = element_text(margin = margin(r = 50)),axis.title.x = element_text(margin = margin(t = 20)))+
  theme(axis.text.x = element_text(face ="bold",color="black",angle=0,vjust=1))