R/Gramm.R

In gramm4R: Generalized correlation analysis and model construction strategy for metabolome and microbiome

Gramm<-function(A,B,C,metaNor=TRUE,rarefaction=FALSE,r=0.5,alpha=0.05){
  xdatag<-as.data.frame(A@assays@data@listData$counts)
  xnameg<-as.character(A@elementMetadata@listData$X)
  AAA<-cbind(xnameg,xdatag)

  ydatag<-as.data.frame(B@assays@data@listData$counts)
  ynameg<-as.character(B@elementMetadata@listData$X)
  BBB<-cbind(ynameg,ydatag)

    preresult<-preGramm(A,B,metaNor,rarefaction)
    xpos<-preresult$x
    ypos<-preresult$y
    nlfitGramstop<-function(X,Y){
    Xdata<-X[,-1]
    Ydata<-Y[,-1]
    Xname<-X[,1]
    Yname<-Y[,1]
    modellist<-c("line2P","line3P","log2P","exp2P","exp3P","power2P","power3P")
    for(i in seq_len(nrow(Xdata))){
    for(j in seq_len(nrow(Ydata))){
        xx<-as.numeric(Xdata[i,])
        yy<-as.numeric(Ydata[j,])
        yadj <- yy - min(yy) + 1
        zzz <- data.frame(xx, yadj)
        n = length(xx)
        k = 3
        r2<--2
        tryCatch({
        fit <- nls(yadj ~ SSlogis(xx,a,b,c),data=zzz)
        sum.exp3P <- summary(fit)
        ss.res <- sum((residuals(fit))^2)
        ss.total.uncor <- sum(yy^2)
        ss.total.cor <- sum((yy - mean(yy))^2)
        ss.reg <- ss.total.cor - ss.res
        dfR = k - 1
        dfE = n - k
        Fval = (ss.reg/dfR)/(ss.res/dfE)
        pval = pf(Fval, dfR, dfE, lower.tail = FALSE)
        pval <- unname(pval)
        RSE <- sum.exp3P$sigma
        SSE <- (RSE^2) * (n - 1)
        adjr2 <- 1 - SSE/((var(yy)) * (n - 1))
        r2 <- 1 - (1 - adjr2) * ((n - k)/(n - 1))
        r2 = format(r2, digits = 5)
        r2 = as.numeric(r2)
        },error=function(e){cat("S curve ERROR :",conditionMessage(e),"\n")})

        if(r2<0){
        fitr2<-matrix(NA,2,7)
        for(m in seq_len(7)){
        tryCatch({
        t1<-basicTrendline::trendline_summary(as.numeric(Xdata[i,]),
                      as.numeric(Ydata[j,]),model =modellist[m] )
        fitr2[1,m]<-t1$R.squared
        fitr2[2,m]<-m
        },error=function(e){cat("ERROR :",conditionMessage(e),"\n")})
        }
        maxr2<-which.max(fitr2[1,])
        tryCatch(
            {
            basicTrendline::trendline(as.numeric(Xdata[i,]),as.numeric(Ydata[j,]),
            model = modellist[maxr2],xlab = Xname[i],ylab = Yname[j])

            },error=function(e){cat("ERROR :",conditionMessage(e),"\n") }
        )
        }
        else{
        fitr2<-matrix(NA,2,7)
        for(m in seq_len(7)){
        tryCatch({
        t1<-basicTrendline::trendline_summary(as.numeric(Xdata[i,]),
                             as.numeric(Ydata[j,]),model =modellist[m] )
        fitr2[1,m]<-t1$R.squared
        fitr2[2,m]<-m
        },error=function(e){cat("ERROR :",conditionMessage(e),"\n")})
        }
          #contrast s with 7 curves r2
        if(r2>max(fitr2[1,],na.rm = TRUE)){
        param<- vector("expression", 2)
        aa<-coef(fit)[1]
        aa<-unname(aa)
            aa<-format(aa,digits = 5)
            aa<-as.character(aa)
            bb<-coef(fit)[2]
            bb<-unname(bb)
            bb<-format(bb,digits = 5)
            bb<-as.character(bb)
            cc<-coef(fit)[3]
            cc<-unname(cc)
            cc<-format(cc,digits = 5)
            cc<-as.character(cc)
            pval<-format(pval, digits = 5)
            pval <- paste("=", unname(pval))
            rval <- paste("=", unname(r2))
            expression(italic("y") ==frac(aa,1+ ~ italic("e")^(frac(bb~-x,cc))))
param[1]<-bquote(expression(italic("y") ==frac(.(aa),
                            1+ ~ italic("e")^(frac(.(bb)~-x,.(cc))))))[2]
param[2]  <- bquote(expression(italic("R")^2 ==.(r2)* "," ~ ~italic("p") ~ ~.(pval) ))[2]
            #substitute(expression(italic("R")^2 == r2 * "," ~ ~italic("p") ~ ~pval ))[2]

            investr::plotFit(fit,interval = "confidence", shade = TRUE,
                             col.fit = "blue",xlab = Xname[i],ylab = Yname[j])

            legend("topleft",  legend = param,  cex = 1, bty = "n")

          }
            else{
            maxr2<-which.max(fitr2[1,])
            tryCatch(
              {
             basicTrendline::trendline(as.numeric(Xdata[i,]),as.numeric(Ydata[j,]),
             model = modellist[maxr2],xlab = Xname[i],ylab = Yname[j])

             },error=function(e){cat("ERROR :",conditionMessage(e),"\n") }
            )
          }
        }
      }
    }




  }
    #minerva


    uniresult<-naiveGramm(A,B,C,r,alpha)
    #uniresult<-naiveGramm1(xpos,ypos,C,r,alpha)
    result_score_loading<-list()
    unir<-uniresult$r
    max10<-arrayInd(order(unir,decreasing=TRUE)[seq_len(10)],dim(unir))
    pdf("R value top 10 pairs.pdf")
    for(top in seq_len(10)){
    xtop<-AAA[max10[top,1],]
    ytop<-BBB[max10[top,2],]
    nlfitGramstop(xtop,ytop)
}
    dev.off()
    resultsall<-list()
    resultsall[["pretreatment"]]<-preresult
    resultsall[["correlation"]]<-uniresult
}