R/ttmap_sgn_genes.R

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

ttmap_sgn_genes <-
function(ttmap_part2_gtlmap, ttmap_part1_hda, 
ttmap_part1_ctrl_adj, c, n = 2, a = 0, filename = "TEST2",
annot = ttmap_part1_ctrl_adj$tag.pcl, col = "NAME",
path = getwd(), Relaxed = 1) {
    setwd(path)
    dir.create(paste(getwd(), "all", sep = "/"))
    dir.create(paste(getwd(), "mid1", sep = "/"))
    dir.create(paste(getwd(), "mid2", sep = "/"))
    dir.create(paste(getwd(), "high", sep = "/"))
    dir.create(paste(getwd(), "low", sep = "/"))
    if(Relaxed != 1) {
        ttmap_sgn_genes_inter <- ttmap_sgn_genes_inter2
        }
    junk_low <- list(x = 0)
    for(i in seq_len(length(ttmap_part2_gtlmap$low_map))){
        A <- ttmap_sgn_genes_inter(ttmap_part2_gtlmap$low_map[[i]],
        ttmap_part1_hda, alpha = a)
        A <- as.matrix(A)
        A <- cbind(as.character(annot[rownames(A), col]), A)
        write.table(A, file = paste(paste("low",
        filename, sep = "/"),
        paste(c[ttmap_part2_gtlmap$low_map[[i]][1], n],
        "txt", sep = "."), sep = "_"),
        quote = FALSE, sep = "\t", 
        row.names = TRUE, col.names = NA)
    }
    for(i in seq_len(length(ttmap_part2_gtlmap$mid1_map))){
        A <- ttmap_sgn_genes_inter(ttmap_part2_gtlmap$mid1_map[[i]],
        ttmap_part1_hda, alpha = a)
        A <- as.matrix(A)
        A <- as.data.frame(A)
        A <- cbind(annot[rownames(A), col], A)
        write.table(A, file=paste(paste("mid1",
        filename, sep = "/"),
        paste(c[ttmap_part2_gtlmap$mid1_map[[i]][1], n],
        "txt", sep = "."), sep = "_"),
        quote = FALSE, sep = "\t", 
        row.names = TRUE, col.names = NA)
    }
    for(i in seq_len(length(ttmap_part2_gtlmap$mid2_map))){
        A <- ttmap_sgn_genes_inter(ttmap_part2_gtlmap$mid2_map[[i]],
        ttmap_part1_hda, alpha = a)
        A <- as.matrix(A)
        A <- as.data.frame(A)
        A <- cbind(annot[rownames(A), col], A)
        write.table(A, file = paste(paste("mid2", 
        filename, sep = "/"),
        paste(c[ttmap_part2_gtlmap$mid2_map[[i]][1], n], 
        "txt", sep = "."),
        sep = "_"), quote = FALSE, sep = "\t", row.names = TRUE,
        col.names = NA)
    }
    for(i in seq_len(length(ttmap_part2_gtlmap$high_map))){
        A <- ttmap_sgn_genes_inter(ttmap_part2_gtlmap$high_map[[i]],
        ttmap_part1_hda, alpha = a)
        A <- as.matrix(A)
        A <- as.data.frame(A)
        A <- cbind(annot[rownames(A), col], A)
        write.table(A, file=paste(paste("high", filename, sep = "/"),
        paste(c[ttmap_part2_gtlmap$high_map[[i]][1],n], 
        "txt", sep = "."),
        sep = "_"), quote = FALSE,
        sep = "\t", row.names = TRUE, col.names = NA)
    }
    for(i in seq_len(length(ttmap_part2_gtlmap$all))){
        A <- ttmap_sgn_genes_inter(ttmap_part2_gtlmap$all[[i]],
        ttmap_part1_hda, alpha = a)
        A <- as.matrix(A)
        A <- as.data.frame(A)
        if(dim(A)[2] == 1){ colnames(A) <- ttmap_part2_gtlmap$all[[i]]}
        A <- cbind(annot[rownames(A), col], A)
        write.table(A, file = paste(paste("all", filename, sep = "/"),
        paste(c[ttmap_part2_gtlmap$all[[i]][1], n],
        "txt",sep = "."), sep = "_"),
        quote = FALSE, sep = "\t", row.names = TRUE, 
        col.names = NA)
    }
}