stage

extra/scripts/genome.rd7.R

@@ -0,0 +1,28 @@
+.pkgname <- "genome.rd7"
+.seqnames <- paste("chr", c(1:22, "X", "Y"), sep = "")
+.circ_seqs <- "chrD"
+.mseqnames <- NULL
+
+.onLoad <- function(libname, pkgname) {
+	if (pkgname != .pkgname)
+		stop("package name (", pkgname, ") is not ", "the expected name (", .pkgname, ")")
+	extdata_dirpath <- system.file("gendata", package = pkgname, lib.loc = libname, mustWork = TRUE)
+	bsgenome <- BSgenome(
+		organism = "Unknown",
+		species = "unk",
+		provider = "UCSC",
+		provider_version = "hg19",
+		release_date = "July 2019",
+		release_name = "Genome",
+		seqnames = .seqnames,
+		circ_seqs = .circ_seqs,
+		mseqnames = .mseqnames,
+		seqs_pkgname = pkgname,
+		seqs_dirpath = extdata_dirpath
+	)
+	ns <- asNamespace(pkgname)
+
+	objname <- pkgname
+	assign(objname, bsgenome, envir = ns)
+	namespaceExport(ns, objname)
+}

extra/scripts/viz-gen.R

@@ -2,8 +2,8 @@ library(ggbio)
 library(GenomicRanges)
 p <- ggbio()
 data("CRC", package = "biovizBase")
-head(hg19sub)
-p <- ggbio() + circle(hg19sub, geom = "ideo", fill = "gray70") +
-	+ circle(hg19sub, geom = "scale", size = 2) +
-	+ circle(hg19sub, geom = "text", aes(label = seqnames), vjust = 0, size = 3)
+head(hg18sub)
+p <- ggbio() + circle(hg19sub, geom = "ideo", fill = "yellow") +
+	 circle(hg19sub, geom = "scale", size = 3) +
+	 circle(hg19sub, geom = "text", aes(label = seqnames), vjust = 10, size = 3)
 p