R/plot.SeqAcnucWeb.R

In seqinr: Biological Sequences Retrieval and Analysis

################################################################################
#
#                              plot.SeqAcnucWeb
#
################################################################################

plot.SeqAcnucWeb <- function(x, types = getType()$sname, socket = autosocket(), ...){
    verbose <- FALSE # a passer en argument si besoin est
    #
    # Check arguments:
    #
    if(!inherits(x, "SeqAcnucWeb")) stop("Sequence of class SeqAcnucWeb is needed")
    
    #
    # Save graphical parameters:
    #
    old.par <- graphics::par(no.readonly = TRUE)
    on.exit(graphics::par(old.par))
    
    if(verbose) cat(paste("types:", types, sep = "\n"))
    
    #
    # Get the parent sequence:
    #
    
    GiveMeTheMotherSequence <- paste("me n=", x, sep = "") 
    query(listname = "me", query = GiveMeTheMotherSequence, socket = socket)
    MotherLength <- as.numeric(getLength(get("me", .seqinrEnv)$req[[1]]))
    MotherName <- get("me", .seqinrEnv)$req[[1]]
    if(verbose) cat("\nMotherLength = ", MotherLength)
    
    #
    # Plot organization:
    #
    graphics::par(mar = c(2.1, 0.1, 4.1, 0.1), lend = "square", ljoin = "mitre")
    cx <- c(0, MotherLength)
    cy <- c(0, 1)
    graphics::plot(cx, cy, ann = FALSE, type = "n", axes = FALSE)
    graphics::axis(1)
    graphics::title(main = paste("Physical position of subsequences on the parent sequence",
                       MotherName, "(", MotherLength, "bp )", sep=" "))
    
    #
    # Look for subsequences:
    #
    
    GiveMeAllSubsequences <- paste("fi n=", MotherName, sep = "")
    query(listname = "filles", query = GiveMeAllSubsequences, socket = socket)
    
    n <- length(types) # number of potential subsequences types
    ispresent <- rep(FALSE, n) # will be TRUE if one or more subsequence of this type is found
    nb <- numeric(n) # count of subsequences for available types
    posi <- vector(mode = "list", length = n) # position of subsequences
    
    for(i in seq_len(n)){
        q <- paste("filles et t=", types[i], sep = "")
        if(verbose) cat("query = ", q, "\n")
        
        result <- try(query(socket = socket, listname = "tmp", query = q))
        if( inherits(result, "try-error")) next
        if(get("tmp", .seqinrEnv)$nelem == 0) next
        if(is.na(get("tmp", .seqinrEnv)$req[[1]])) next
        if(get("tmp", .seqinrEnv)$req[[1]] == x ) next
        
        ispresent[i] <- TRUE
        
        u <- lapply(get("tmp", .seqinrEnv)$req, getLocation)
        names(u) <- get("tmp", .seqinrEnv)$req
        nb[i] <- length(u)
        posi[[i]] <- u
    }
    
    #
    # Draw subsequences:
    #
    posi <- posi[ispresent]
    nb <- nb[ispresent]
    types <- types[ispresent]
    n <- length(types)
    for(i in seq_len(n)){
        for(j in seq_len(length(posi[[i]]))){
            xleft <- posi[[i]][[j]][1]
            ybottom <- (i - 1)/(n + 1)
            xright <- posi[[i]][[j]][2]
            ytop <- i/(n + 1)
            graphics::rect(xleft, ybottom, xright, ytop, col = i, border = "black", lend = "square", ljoin = "mitre" )
        }
    }
    
    #
    # Draw legend:
    #
    graphics::legend("top", legend = paste(types, "(", nb, ")", sep = ""), fill = seq_len(n), horiz = TRUE, bty = "n")
    
    resu <- lapply(posi,function(x){lapply(x,unlist)})
    names(resu) <- types
    
    #
    #  workspace cleanup
    #
    
    rm("me", pos = .seqinrEnv)
    rm("filles", pos = .seqinrEnv)
    rm("tmp", pos = .seqinrEnv)
    
    #
    # Return invisibly the result:
    #
    invisible(resu)
}