Heatmap of correlation between physical and chemical factors and microbial abundance.Rmd

---
title: "Heatmap of correlation between physical and chemical factors and microbial abundance"
author: "xyz"
date: "2020/5/2"
output: html_document
---

```{r}
# phylum level
df<-read.table("X101SC19050239-Z01-F001-B1-41_result/02.OTUanalysis/taxa_abundance/Absolute/otu_table.p.absolute.xls",
               header = T)
metaData<-readxl::read_xlsx("metaData.xlsx")
env<-metaData[,-1:-3]
# the physical and chemical factors are logarithmic
env.log10<- log1p(env)
otu <- t(df[,c(-1,-56)])
colnames(otu)<-df$Taxonomy
# relative abundance
otu.prop<-prop.table(otu,1)
library("psych")
results<-corr.test(otu.prop,env.log10)
# Screen for phyla with significant correlation
ix<-results$p
ix<-ix<0.05
ix<-rowSums(ix)>0
significance<-function(x){
  if(x>=0.05)
  ""
  else if (x>=0.01)
  "*"
  else "**"
}
result.significance<-matrix(sapply(results$p[ix,],significance),nrow=sum(ix))
pheatmap::pheatmap(results$r[ix,], cluster_row=T,scale="row",fontsize = 20,
                   # pix=width\height*300, col label angle_col = "45"
                   filename ="Heatmap of correlation between physical and chemical factors and phyla abundance.png",
                   width=10,height = 6,
                   display_numbers=result.significance)
# Total abundance
# Firmicutes                Bacteroidetes                Nitrospirae              Gracilibacteria 
# 108555                    98948                        27690                         1765 
# Fibrobacteres             Elusimicrobia Candidatus_Jorgensenbacteria         unidentified_Archaea 
# 1102                      1375                         1028                          312 
# Berkelbacteria            Parcubacteria  Candidatus_Yanofskybacteria Candidatus_Magasanikbacteria 
# 491                       387                          306                           89 
colSums(otu[,ix])
# relative abundance
 #                  Firmicutes                Bacteroidetes                  Nitrospirae              Gracilibacteria 
 #                 5.453367192                  4.970750099                  1.391034384                  0.088666511 
 #               Fibrobacteres                Elusimicrobia Candidatus_Jorgensenbacteria         unidentified_Archaea 
 #                 0.055360054                  0.069074477                  0.051642591                  0.015673627 
 #              Berkelbacteria                Parcubacteria  Candidatus_Yanofskybacteria Candidatus_Magasanikbacteria 
 #                 0.024665868                  0.019441326                  0.015372211                  0.004471003 
(colSums(otu)/sum(otu))[ix]*100
```