test_cov_wide_gr: Sample exon coverage data GRanges with wide introns

In jmw86069/splicejam: Analysis and Visualization of Gene Splice Variants and Transcriptome Data

Sample exon coverage data GRanges with wide introns

Description

Sample exon coverage data GRanges with wide introns

Usage

test_cov_wide_gr

Format

An object of class GRanges of length 4.

Details

This dataset represents exon GRanges with an additional column with NumericList values representing RNA-seq read coverage across these exons.

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_exon_gr, test_exon_wide_gr, test_junc_gr, test_junc_wide_gr

Examples

# The steps below demonstrate how to create coverage data manually
suppressPackageStartupMessages(library(GenomicRanges));
suppressPackageStartupMessages(library(ggplot2));

data(test_cov_gr);
data(test_exon_wide_gr);
test_cov_wide_gr <- test_cov_gr;
ranges(test_cov_wide_gr) <- ranges(test_exon_wide_gr);

# You can plot coverage using exoncov2polygon()
widecovdf <- exoncov2polygon(test_cov_wide_gr, covNames="sample_A");
ggWide3 <- ggplot(widecovdf,
      aes(x=x, y=y, group=gr, fill=gr, color=gr)) +
   ggforce::geom_shape(alpha=0.7) +
   colorjam::theme_jam() +
   colorjam::scale_fill_jam() +
   colorjam::scale_color_jam();
print(ggWide3);

# Now compress the introns keeping axis labels
ref2c <- make_ref2compressed(test_cov_wide_gr,
   nBreaks=10);
ggWide3c <- ggWide3 +
   scale_x_continuous(trans=ref2c$trans_grc) +
   xlab("chr1 (compressed introns)") +
   ggtitle("exons (compressed introns)");
print(ggWide3c);

# you can add junctions to exons in one plot
junc_wide_c_df <-grl2df(test_junc_wide_gr,
   shape="junction",
   ref2c=ref2c);
ggWide3c +
   ggforce::geom_diagonal_wide(data=junc_wide_c_df,
      inherit.aes=FALSE,
      show.legend=FALSE,
      fill="orange",
      aes(x=x, y=y, group=id),
      alpha=0.6)

jmw86069/splicejam documentation built on Nov. 4, 2024, 10:53 a.m.