R/getVenn.R

In yufree/xMSannotator: xMSannotator: R package for network based annotation of metabolomics data.

getVenn <- function(dataA, name_a, dataB, name_b, mz.thresh = 10, 
    time.thresh = 30, alignment.tool = NA, xMSanalyzer.outloc, 
    use.unique.mz = FALSE, plotvenn = TRUE, num_nodes = 2) {
    dir.create(xMSanalyzer.outloc, showWarnings = FALSE)
    
    plotvenn = FALSE
    data_a <- as.data.frame(dataA)
    data_b <- as.data.frame(dataB)
    rm(dataA)
    rm(dataB)
    
    common <- {
    }
    commonA <- {
    }
    commonB <- {
    }
    
    ############################################ 
    
    if (use.unique.mz == TRUE) {
        data_a <- find.Unique.mzs.sameset(dataA = data_a, 
            dataB = data_a, mz.thresh = mz.thresh, time.thresh = time.thresh, 
            alignment.tool = alignment.tool)
        data_a <- data_a$uniqueA
        
        # print(dim(data_a))
        
        data_b <- find.Unique.mzs.sameset(dataA = data_b, 
            dataB = data_b, mz.thresh = mz.thresh, time.thresh = time.thresh, 
            alignment.tool = alignment.tool)
        data_b <- data_b$uniqueA
    }
    
    
    # common<-find.Overlapping.mzs(data_a,data_b,mz.thresh,time.thresh=time.thresh,alignment.tool=alignment.tool)
    
    # save(list=ls(),file='overlap.Rda')
    
    common <- find.Overlapping.mzsvparallel(data_a, data_b, 
        mz.thresh, time.thresh = time.thresh, alignment.tool = alignment.tool, 
        num_nodes = num_nodes)
    
    if (is.na(time.thresh) == FALSE) {
        mznames = c("index.A", "mz.data.A", "time.data.A", 
            "index.B", "mz.data.B", "time.data.B", "time.difference")
        
    } else {
        mznames = c("index.A", "mz.data.A", "index.B", "mz.data.B")
    }
    
    if (length(common) > 0) {
        # commonA<-data_a[c(common$index.A),]
        # commonA<-unique(commonA)
        
        # commonB<-data_b[c(common$index.B),]
        # commonB<-unique(commonB)
        
        # colnames(common)<-c('index.A','mz.data.A','index.B','mz.data.B')
        
        colnames(common) <- mznames
    } else {
        
        num_common <- 0
        commonA <- {
        }
        commonB <- {
        }
    }
    
    
    return(list(common = common))
    # ,'commonA'=commonA,'commonB'=commonB))
    
}