R/safedag.R

In safe: Significance Analysis of Function and Expression

safedag <-
function (object = NULL, ontology = NULL, top = NULL,
    color.cutoffs = c(0.1, 0.01, 0.001), filter = 0, max.GOnames = 200)
{
    require("GOstats")
    require("Rgraphviz")
    if (is.null(ontology)) {
        ontology <- Ontology(mget(names(object@global.stat)[1],
            GOTERM)[[1]])
        cat(paste("Ontology unspecified so assumed to be GO.",
            ontology, "\n", sep = ""))
    }
    else if (!ontology %in% c("GO.CC", "GO.BP", "GO.MF")) {
        stop("ontology must be \"GO.CC\", \"GO.BP\", or \"GO.MF\"",
            call. = FALSE)
        ontology = substr(ontology, 4, 5)
    }
    if (!is.null(top)) {
        keep2 <- top
        stop <- 0
        names <- names(as.list(get(paste("GO", ontology, "CHILDREN",
            sep = ""))))
        while (stop == 0) {
            parents <- keep2[keep2 %in% names]
            children <- unlist(mget(parents, get(paste("GO",
                ontology, "CHILDREN", sep = ""))))
            stop <- all(children %in% keep2)
            keep2 <- unique(c(keep2, children))
        }
    }
    else {
        top <- c("GO:0005575", "GO:0008150", "GO:0003674")[c("CC",
            "BP", "MF") %in% ontology]
        keep2 <- NULL
    }
    parents <- get(paste("GO", ontology, "PARENTS", sep = ""))
    C.names <- names(object@global.stat)
    keep <- C.names %in% names(as.list(parents))
    cat(paste(sum(keep), " of ", length(C.names), " categories in GO.",
        ontology, "\n", sep = ""))
    if (!is.null(keep2)) {
        keep[!C.names %in% keep2] <- FALSE
        cat(paste(sum(keep), "of", length(C.names), "categories below",
            top, "\n"))
    }
    p <- object@global.pval
    cat(paste("\n", sum(p <= color.cutoffs[3]), "categories with p <=",
        color.cutoffs[3], "\n"))
    if (filter < 3)
        cat(paste("", sum(p <= color.cutoffs[2]), "categories with p <=",
            color.cutoffs[2], "\n"))
    if (filter < 2)
        cat(paste("", sum(p <= color.cutoffs[1]), "categories with p <=",
            color.cutoffs[1], "\n"))
    if (filter)
        keep[p > color.cutoffs[filter]] <- FALSE
    color <- 8 - (p <= color.cutoffs[1]) * 6 + (p <= color.cutoffs[2]) +
        (p <= color.cutoffs[3])
    g <- GOGraph(C.names[keep], parents)
    nda <- makeNodeAttrs(g)
    nodes <- names(nda$fillcolor)
    if (is.null(keep2))
        g <- subGraph(nodes[!nodes %in% c("all", "top")], g)
    else g <- subGraph(nodes[nodes %in% keep2], g)
    nda <- makeNodeAttrs(g)
    nodes <- names(nda$fillcolor)
    match <- match(nodes, C.names[keep], nomatch = 0)
    nda$fillcolor[match] <- color[keep]
    nda$fillcolor[!nodes %in% C.names] <- "white"
    if (length(nodes) > max.GOnames)
        nda$label[nda$label != ""] <- " "
    else {
        if (is.null(keep2))
            nda$label[nodes == top] <- ontology
    }
    g <- agopen(g, nodeAttrs = nda, name = "whatever")
    par(mfrow = c(1, 1))
    plot(g)

}