Sample exon data GRanges with wide introns

Sample exon data GRanges with wide introns

test_exon_wide_gr

Format

GRanges object where each segment represents one exon for an arbitrary gene. It has one column of values, "gene_name" used for Sashimi plot preparation.

Details

This dataset contains RNA-seq splice junction data stored as a GRangesList.

Intron and exon sizes are more consistent with mammalian gene structure, and are intended to demonstrate the challenge with visualizing exon coverage data on a genomic scale. See examples for steps to compress the intron sizes.

See also

Other splicejam data: test_cov_gr, test_cov_wide_gr, test_exon_gr, test_junc_gr, test_junc_wide_gr

Examples

# The code below is used to create the exon test data
suppressPackageStartupMessages(library(GenomicRanges));
suppressPackageStartupMessages(library(ggplot2));

test_exon_wide_gr <- GRanges(seqnames=rep("chr1", 4),
   ranges=IRanges::IRanges(
      start=c(100, 10300, 20500,  39900),
        end=c(200, 10400, 20750, 40000)),
   strand=rep("+", 4),
   gene_name=rep("TestGene1", 4));
names(test_exon_wide_gr) <- jamba::makeNames(rep("wide", length(test_exon_wide_gr)),
   suffix="");
test_exon_wide_gr;
#> GRanges object with 4 ranges and 1 metadata column:
#>         seqnames      ranges strand |   gene_name
#>            <Rle>   <IRanges>  <Rle> | <character>
#>   wide1     chr1     100-200      + |   TestGene1
#>   wide2     chr1 10300-10400      + |   TestGene1
#>   wide3     chr1 20500-20750      + |   TestGene1
#>   wide4     chr1 39900-40000      + |   TestGene1
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths

# To plot a simple GRanges object
widedf <- grl2df(test_exon_wide_gr);
#> Warning: failed to set names on the unlisted CompressedRleList object
ggWide <- ggplot(widedf, aes(x=x, y=y, group=id, fill=feature_type)) +
   geom_polygon() +
   colorjam::theme_jam() +
   colorjam::scale_fill_jam() +
   xlab("chr1") +
   ggtitle("exons (full introns)")
print(ggWide);

# Now compress the introns keeping axis labels
ref2c <- make_ref2compressed(test_exon_wide_gr,
   nBreaks=10);
ggWide2 <- ggWide +
   scale_x_continuous(trans=ref2c$trans_grc) +
   xlab("chr1 (compressed introns)") +
   ggtitle("exons (compressed introns)")
print(ggWide2);