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Fig.4AB.Manhatanplot.drought.Rmd
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---
title: "Untitled"
author: "Cheng Gao"
date: "4/5/2019"
output: html_document
---
```{r, message=FALSE, warning=FALSE, fig.height = 8, fig.width = 12, fig.align = "center"}
# Manhatan drought
library(ggrepel)
library(vegan)
library(dplyr)
rm(list = ls())
load("EPICON.data.preparation.RC.bNTI.ted.2019.04.19.Rdata")
otu_table0<-data.frame(t(fung.raw)) ##Read in the raw data###
row.names(otu_table0)<-row.names(ID)
otu_table1<-data.frame(t(otu_table0[ID$Kingdom=="Fungi",]))
env$Treatment1<-factor(env$Treatment1,levels=c("Control", "Pre_flowering_drought", "Post_flowering_drought"))
manhatan.drought<- function (habitat,tp, Ntreat, treat)
{
fung<-otu_table1[env$Habitat == habitat, ]
fung<-fung[,colSums(fung)>0]
subse<- env$Habitat == habitat & env$TP> tp & env$Treatment1 != Ntreat
fung.subs<-otu_table1[subse,]
set.seed(315)
fung.subs<-data.frame(rrarefy(fung.subs, min(rowSums(fung.subs))))
com<-fung.subs[,colSums(fung.subs)>0]
env.subs<-env[subse,]
va<-env.subs[, treat]
paov<-adonis(com~va)
print(paov)
dvoc<-data.frame()
for (i in c(1: ncol(com)))
{
tt<-t.test(com[,i]~va) # t test
p<-tt$p.value # pvalue of t test
name<-colnames(com)[i] # OTU name
fs<-aggregate(com[,i], by=list(va), FUN=mean) # mean abundance of OTU in two habitats
fc<-log2((fs[1,2]+1)/(fs[2,2]+1))
abu<-log2(colSums(com)[i]/nrow(com)+1)
dd<-data.frame(fc,p, name,abu, i, " ")
dvoc<-rbind(dvoc, dd)
}
dvoc<-data.frame(dvoc)
names(dvoc)<-c("log2FoldChange", "pvalue","name", "log2AverageAbundance", "order", "Group")
dvoc$padj<-p.adjust(dvoc$pvalue, n = length(dvoc$pvalue))
dvoc$neglogp = -log(dvoc$pvalue)
dvoc$level = as.factor(ifelse( dvoc$log2FoldChange > 0, "Control > Drought", "Drought > Control"))
dvoc$level<-factor(dvoc$level,levels=c("Control > Drought","Drought > Control"))
x<-droplevels(merge(dvoc,ID, by.y = "OTU.ID.1", by.x = "name", all = FALSE))
x = arrange(x, Guild,Genus,log2AverageAbundance,neglogp)
x<-x[order(x$Guild),]
x$name = factor(x$name, levels=x$name)
x1<-droplevels(x[x$neglogp >=10,])
pos<-droplevels(x1[x1$log2FoldChange>0,])
neg<-droplevels(x1[x1$log2FoldChange<0,])
print(pos$name)
print(neg$name)
x$Guild<-factor(x$Guild, labels = c("Arbuscular mycorrhiza", "Endophyte", "Plant pathogen", "Plant pathogen (Yeast)", "Saprotroph", "Saprotroph (Yeast)", "Others"))
p1<-ggplot(x, aes(x=name, y=neglogp, color=Guild, size=log2AverageAbundance, shape=level)) +
geom_point(alpha = 0.5, stroke = 1.5) +
geom_text_repel(data=subset(x, neglogp > 10),vjust="inward",hjust="inward",
aes(label=Genus), angle = 0, size=3, color="black",fontface= "bold")+
geom_hline(yintercept= 10, linetype=1, color="green") +
scale_shape_manual(values=c(1, 2))+
scale_size(breaks=c(5, 10, 15)) +
labs(x=" ", y=" ") +
scale_color_manual(values=c("green","blue","purple","black","chocolate", "red","grey"))+
theme(axis.ticks.x=element_blank(),axis.text.x=element_blank())+
theme(panel.background = element_rect(fill = NA)) +
labs(title = habitat, x = "", y=" ", size = "log(Average Abundance)", shape = "Drought effect") +
theme(legend.title = element_text(colour="black", size=15, face="bold"),
legend.text = element_text(colour="black", size=15, face="bold"),
axis.line = element_line(linetype = "solid"),
axis.text=element_text(size=10,face="bold"),
axis.title=element_text(size=15,face="bold"))
return(p1)
}
manhatan.drought("Leaf", 2, "Post_flowering_drought","Treatment1" )
manhatan.drought("Leaf", 9, "Pre_flowering_drought","Treatment1" )
manhatan.drought("Root", 2, "Post_flowering_drought","Treatment1" )
manhatan.drought("Root", 9, "Pre_flowering_drought","Treatment1" )
manhatan.drought("Rhizosphere", 2, "Post_flowering_drought","Treatment1" )
manhatan.drought("Rhizosphere", 9, "Pre_flowering_drought","Treatment1" )
manhatan.drought("Soil", 2, "Post_flowering_drought","Treatment1" )
manhatan.drought("Soil", 9, "Pre_flowering_drought","Treatment1" )
```
```{r, message=FALSE, warning=FALSE, fig.height = 3, fig.width = 3, fig.align = "center"}
manhatan.drought<- function (habitat,tp, Ntreat, treat)
{
fung<-otu_table1[env$Habitat == habitat, ]
fung<-fung[,colSums(fung)>0]
subse<- env$Habitat == habitat & env$TP> tp & env$Treatment1 != Ntreat
fung.subs<-otu_table1[subse,]
set.seed(315)
fung.subs<-data.frame(rrarefy(fung.subs, min(rowSums(fung.subs))))
com<-fung.subs[,colSums(fung.subs)>0]
env.subs<-env[subse,]
va<-env.subs[, treat]
paov<-adonis(com~va)
print(paov)
dvoc<-data.frame()
for (i in c(1: ncol(com)))
{
tt<-t.test(com[,i]~va) # t test
p<-tt$p.value # pvalue of t test
name<-colnames(com)[i] # OTU name
fs<-aggregate(com[,i], by=list(va), FUN=mean) # mean abundance of OTU in two habitats
fc<-log2((fs[1,2]+1)/(fs[2,2]+1))
abu<-log2(colSums(com)[i]/nrow(com)+1)
dd<-data.frame(fc,p, name,abu, i, " ")
dvoc<-rbind(dvoc, dd)
}
dvoc<-data.frame(dvoc)
names(dvoc)<-c("log2FoldChange", "pvalue","name", "log2AverageAbundance", "order", "Group")
dvoc$padj<-p.adjust(dvoc$pvalue, n = length(dvoc$pvalue))
dvoc$neglogp = -log(dvoc$pvalue)
dvoc$level = as.factor(ifelse( dvoc$log2FoldChange > 0, "Control > Drought", "Drought > Control"))
dvoc$level<-factor(dvoc$level,levels=c("Control > Drought","Drought > Control"))
x<-droplevels(merge(dvoc,ID, by.y = "OTU.ID.1", by.x = "name", all = FALSE))
x = arrange(x, Guild,Genus,log2AverageAbundance,neglogp)
x<-x[order(x$Guild),]
x$name = factor(x$name, levels=x$name)
x1<-droplevels(x[x$neglogp >=10,])
pos<-droplevels(x1[x1$log2FoldChange>0,])
neg<-droplevels(x1[x1$log2FoldChange<0,])
print(pos$name)
print(neg$name)
x$Guild<-factor(x$Guild, labels = c("Arbuscular mycorrhiza", "Endophyte", "Plant pathogen", "Plant pathogen (Yeast)", "Saprotroph", "Saprotroph (Yeast)", "Others"))
p1<-ggplot(x, aes(x=name, y=neglogp, color=Guild, size=log2AverageAbundance, shape=level)) +
geom_point(alpha = 0.5, stroke = 1.5) +
#geom_text_repel(data=subset(x, neglogp > 10),vjust="inward",hjust="inward",
# aes(label=Genus), angle = 0, size=3, color="black",fontface= "bold")+
geom_hline(yintercept= 10, linetype=1, color="green") +
scale_shape_manual(values=c(1, 2))+
scale_size(breaks=c(5, 10, 15)) +
labs(x=" ", y=" ") +
scale_color_manual(values=c("green","blue","purple","black","chocolate", "red","grey"))+
theme(axis.ticks.x=element_blank(),axis.text.x=element_blank())+
theme(panel.background = element_rect(fill = NA),legend.position = "none") +
labs(title = habitat, x = "", y=" ", size = "log(Average Abundance)", shape = "Drought effect") +
theme(legend.title = element_text(colour="black", size=15, face="bold"),
legend.text = element_text(colour="black", size=15, face="bold"),
axis.line = element_line(linetype = "solid"),
axis.text=element_text(size=10,face="bold"),
axis.title=element_text(size=15,face="bold"))
return(p1)
}
manhatan.drought("Leaf", 2, "Post_flowering_drought","Treatment1" )
manhatan.drought("Leaf", 9, "Pre_flowering_drought","Treatment1" )
manhatan.drought("Root", 2, "Post_flowering_drought","Treatment1" )
manhatan.drought("Root", 9, "Pre_flowering_drought","Treatment1" )
manhatan.drought("Rhizosphere", 2, "Post_flowering_drought","Treatment1" )
manhatan.drought("Rhizosphere", 9, "Pre_flowering_drought","Treatment1" )
manhatan.drought("Soil", 2, "Post_flowering_drought","Treatment1" )
manhatan.drought("Soil", 9, "Pre_flowering_drought","Treatment1" )
```