R/generate_correlation.R

In TTMap: Two-Tier Mapper: a clustering tool based on topological data analysis

generate_correlation <-
function(ttmap_part1_hda, select){
    dd <- as.dist((1 - cor(ttmap_part1_hda$Dc.Dmat[select, ])) / 2)
    dd <- as.matrix(dd)
    if(sum(is.na(dd)) != 0){
        for(i in seq_len(dim(dd)[1])){
            for(j in seq_len(dim(dd)[2])){
                if(is.na(dd[i, j]) == TRUE) dd[i,  j] <- 0
            }
        }
    }
    return(dd)
}