make_ref2compressed: Create a ref2compressed function to compress GR gaps

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

Create a ref2compressed function to compress GR gaps

Description

Create a ref2compressed function to compress GR gaps

Usage

make_ref2compressed(
  gr,
  gapWidth = 200,
  keepValues = FALSE,
  upstream = 50000,
  upstreamGapWidth = gapWidth * 3,
  downstream = 50000,
  downstreamGapWidth = gapWidth * 3,
  nBreaks = 7,
  verbose = FALSE,
  ...
)

Arguments

gr	GRanges object containing regions not to compress. Regions which are unstranded gaps are compressed to fixed width.
gapWidth	integer value used for fixed gap width, or when NULL the gap width is defined as 3 times the median feature width.
keepValues	logical indicating whether to keep feature values in the GRanges data.
upstream, downstream, upstreamGapWidth, downstreamGapWidth	used to define the compression of coordinates upstream and downstream the supplied GRanges. In reality, the upstream range and upstream gap width defines a multiplier, and all upstream coordinates are compressed through zero. Similarly, all downstream coordinates are compressed to 10 billion, which is roughly 3 times the size of the human genome.
nBreaks	the default number of x-axis coordinate breaks used in ggplot labeling.
verbose	logical indicating whether to print verbose output.
...	additional arguments are ignored.

Details

This function takes a set of GRanges which are to be maintained with fixed aspect ratio, and it defines a function to compress coordinates of the gaps between GRanges features.

Value

list with trans_grc which is class "trans" suitable for use in ggplot2 functions; transform a function that converts chromosome coordinates to compressed coordinates; inverse a function that converts compressed coordinates to chromosome coordinates; scale_x_grc a function used similar to ggplot2::scale_x_continuous() during ggplot2 creation; gr a function that compresses coordinates in a GRanges object; grl a function that compresses coordinates in a GRangesList object. Attributes "lookupCoordDF" is a two-column data.frame with chromosome coordinates and compressed coordinates, which is used to create the other transformation functions via stats::approx(); "gapWidth" the gap width used, since it can be programmatically defined; "gr" the GRanges input data used to train the transformation.

See Also

grl2df(), test_junc_wide_gr

Other jam GRanges functions: addGRLgaps(), addGRgaps(), annotateGRLfromGRL(), annotateGRfromGR(), assignGRLexonNames(), closestExonToJunctions(), combineGRcoverage(), exoncov2polygon(), findOverlapsGRL(), flattenExonsBy(), getFirstStrandedFromGRL(), getGRLgaps(), getGRcoverageFromBw(), getGRgaps(), grl2df(), jam_isDisjoint(), sortGRL(), spliceGR2junctionDF(), stackJunctions()

Other splicejam core functions: exoncov2polygon(), gene2gg(), grl2df(), plotSashimi(), prepareSashimi()

Other jam RNA-seq functions: assignGRLexonNames(), closestExonToJunctions(), combineGRcoverage(), defineDetectedTx(), detectedTxInfo(), exoncov2polygon(), flattenExonsBy(), getGRcoverageFromBw(), groups2contrasts(), internal_junc_score(), makeTx2geneFromGtf(), prepareSashimi(), runDiffSplice(), sortSamples(), spliceGR2junctionDF()

Examples

suppressPackageStartupMessages(library(GenomicRanges));
suppressPackageStartupMessages(library(ggplot2));

data(test_exon_wide_gr);
# To plot a simple GRanges object
widedf <- grl2df(test_exon_wide_gr);
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 (introns as-is)")
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);

jmw86069/splicejam documentation built on April 14, 2025, 3:12 a.m.