Nothing
################################
# gene class and methods
################################
# deprecated
## gene <- function(name, start, end, strand, col=NULL, lwd=1, lty=1, pch=8, cex=1,
## gene_type="arrows"){
## if (missing(name)) stop("Name must be provided")
## if (missing(start)) stop ("Start must be provided")
## if (missing(end)) stop ("End must be provided")
## if (missing(strand)) stop ("Strand must be provided")
## gene <- data.frame(name=name, start=start, end=end, strand=strand, col=col,
## lwd=lwd, lty=lty, pch=pch, cex=cex, gene_type=gene_type,
## stringsAsFactors=FALSE)
## as.gene(gene)
## }
## as.gene <- function(gene, col="blue", lwd=1, lty=1, pch=8, cex=1,
## gene_type="arrows"){
## # return self is already of the right class
## if (is.gene(gene)) {
## return(gene)
## }
## # check for presence of arguments
## if (is.null(gene$name)) stop("No gene name")
## if (is.null(gene$start)) stop("No start in gene")
## if (is.null(gene$end)) stop("No end in gene")
## if (is.null(gene$strand)) stop("No strand in gene")
## if (is.null(gene$col)) gene$col <- col
## if (is.null(gene$lwd)) gene$lwd <- lwd
## if (is.null(gene$lty)) gene$lty <- lty
## if (is.null(gene$pch)) gene$pch <- pch
## if (is.null(gene$cex)) gene$cex <- cex
## # gene_type: not given in gene
## if (is.null(gene$gene_type)){
## if (!is.character(gene_type) || !(gene_type %in% gene_types()))
## stop(paste("gene_type muste be one of:",
## paste(gene_types(), collapse=", ")))
## if (gene_type == "auto") gene_type <- "arrows"
## gene$gene_type <- gene_type
## }
## # given in gene
## else {
## if (!is.character(gene$gene_type) || !all(gene_type %in% gene_types()))
## stop(paste("gene_type muste be one of:",
## paste(gene_types(), collapse=", ")))
## }
## # check for correct argument types
## if (!is.character(gene$name)) stop("Non-character name")
## if (!(is.numeric(gene$start) && is.numeric(gene$end)))
## stop("Non-numeric start or end")
## if (!all(is.numeric(c(gene$lwd, gene$lty, gene$pch, gene$cex))))
## stop("lwd, lty, pch and cex must be numeric")
## # care about strand
## if (gene$strand == 1 | gene$strand == "+") {
## gene$strand <- 1
## } else if (gene$strand == -1 | gene$strand == "-") {
## gene$strand <- -1
## } else {
## stop("Invalid gene strand: should be 1, -1, + or -")
## }
## # care about start/end
## if (gene$end < gene$start) stop("End smaller than start. Use strand instead")
## # no color check for the moment
## # convert to df
## gene <- as.data.frame(gene, stringsAsFactors=FALSE)
## # class attribution, no check for other at the moment
## class(gene) <- c("gene", "data.frame")
## gene
## }
## is.gene <- function(gene){
## inherits(gene, "gene")
## }
## # calculates x range
## rang.gene <- function(gene){
## range(c(gene$start, gene$end))
## }
## rang.list <- rang.gene
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