Sample exon coverage data GRanges

test_cov_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.

Examples

suppressPackageStartupMessages(library(GenomicRanges));
suppressPackageStartupMessages(library(ggplot2));
data(test_exon_gr);

# The steps below demonstrate how to create coverage data manually
test_cov_gr <- test_exon_gr;
set.seed(123);
cov_values <- c(250, 200, 180, 250);
values(test_cov_gr)[,"sample_A"] <- NumericList(
   lapply(seq_along(test_exon_gr), function(i){
      cov_values[i] +
         round(rnorm(width(test_exon_gr)[i])*7)
   }));
test_cov_gr;
#> GRanges object with 4 ranges and 2 metadata columns:
#>         seqnames    ranges strand |   gene_name        sample_A
#>            <Rle> <IRanges>  <Rle> | <character>   <NumericList>
#>   exon1     chr1   100-199      + |   TestGene1 246,248,261,...
#>   exon2     chr1   300-399      + |   TestGene1 195,202,198,...
#>   exon3     chr1   500-749      + |   TestGene1 195,189,178,...
#>   exon4     chr1   900-999      + |   TestGene1 260,257,253,...
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths

# You can plot coverage using exoncov2polygon()
exondf <- exoncov2polygon(test_cov_gr, covNames="sample_A");
gg3 <- ggplot(exondf,
      aes(x=x, y=y, group=gr, fill=gr, color=gr)) +
   ggforce::geom_shape(alpha=0.8) +
   colorjam::theme_jam() +
   colorjam::scale_fill_jam() +
   colorjam::scale_color_jam();
print(gg3);

# you can add junctions to exons in one plot
junc_df <- grl2df(test_junc_gr, shape="junction")
gg3 +
   ggforce::geom_diagonal_wide(data=junc_df,
      inherit.aes=FALSE,
      show.legend=FALSE,
      fill="orange",
      aes(x=x, y=y, group=id),
      alpha=0.6)

Sample exon coverage data GRanges

Format

Details

See also

Examples