#FIG1
getwd()
setwd("D:/R work")
rm(list = ls())
#install.packages("readxl")
#install.packages("pheatmap")
library(readxl)
library(pheatmap)
library(psych)
library(reshape2)
microbiota <- data.frame(read_excel("microbiota.xlsx"),stringsAsFactors = FALSE)
rownames(microbiota) =microbiota$sample 
microbiota = microbiota[,-1]
inflammatory <- data.frame(read_excel("inflammatory.xlsx"),stringsAsFactors = FALSE)
rownames(inflammatory) = inflammatory$sample
inflammatory = inflammatory[,-1]
View(microbiota)
head(inflammatory)

cor <- corr.test(microbiota,inflammatory,method="spearman",adjust = "fdr")             
cmt <- cor$r
pmt <- cor$p
cmt.out<-cbind(rownames(cmt),cmt)
pmt.out<-cbind(rownames(pmt),pmt)
df <- melt(cmt,value.name="cor")
df$pvalue <- as.vector(pmt)
head(df)
View(cmt)
if (!is.null(pmt)) {
  ssmt <- pmt < 0.01
  pmt[ssmt] <- '**'
  smt <- pmt > 0.01& pmt <0.05
  pmt[smt] <- '*'
  pmt[!ssmt&!smt] <- ''
} else {
  pmt <- F
}
pheatmap(cmt, 
         scale = "none",
         cluster_row = T, 
         cluster_col = F,               
         display_numbers = pmt, 
         fontsize_number = 12,
         number_color = "white",
         cellwidth = 20,
         cellheight = 20)
pheatmap(cmt, 
         scale = "none", 
         cluster_row = T, 
         cluster_col = F,                
         display_numbers = T, 
         fontsize_number = 12, 
         number_color = "white",
         cellwidth = 20, 
         cellheight = 20)

#FIG2
getwd()
setwd("D:/R work")
rm(list = ls())
#install.packages("readxl")
#install.packages("pheatmap")
library(readxl)
library(pheatmap)
library(psych)
library(reshape2)
microbiota <- data.frame(read_excel("microbiota.xlsx"),stringsAsFactors = FALSE)
rownames(microbiota) =microbiota$sample 
microbiota = microbiota[,-1]
cognitive <- data.frame(read_excel("cognitive.xlsx"),stringsAsFactors = FALSE)
rownames(cognitive) = cognitive$sample
cognitive = cognitive[,-1]
View(microbiota)
head(cognitive)

cor <- corr.test(microbiota,cognitive,method="spearman",adjust = "fdr")             
cmt <- cor$r
pmt <- cor$p
cmt.out<-cbind(rownames(cmt),cmt)
pmt.out<-cbind(rownames(pmt),pmt)
df <- melt(cmt,value.name="cor")
df$pvalue <- as.vector(pmt)
head(df)
View(cmt)
if (!is.null(pmt)) {
  ssmt <- pmt < 0.01
  pmt[ssmt] <- '**'
  smt <- pmt > 0.01& pmt <0.05
  pmt[smt] <- '*'
  pmt[!ssmt&!smt] <- ''
} else {
  pmt <- F
}
pheatmap(cmt, 
         scale = "none",
         cluster_row = T, 
         cluster_col = F,               
         display_numbers = pmt, 
         fontsize_number = 12,
         number_color = "white",
         cellwidth = 20,
         cellheight = 20)
pheatmap(cmt, 
         scale = "none", 
         cluster_row = T, 
         cluster_col = F,                
         display_numbers = T, 
         fontsize_number = 12, 
         number_color = "white",
         cellwidth = 20, 
         cellheight = 20)