grl2df: GRangesList to data.frame for ggplot2

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

GRangesList to data.frame for ggplot2

Description

GRangesList to data.frame for ggplot2

Usage

grl2df(
  grl,
  keepGRvalues = TRUE,
  keepGRLvalues = FALSE,
  addGaps = TRUE,
  width = 0.6,
  widthV = c(exon = 0.6, cds = 0.6, noncds = 0.3, intron = 0.01, gap = 0.01, `NA` = 0.5),
  width_colname = c("subclass", "feature_type"),
  shape = c("rectangle", "junction"),
  baseline = NULL,
  scoreColname = "score",
  sampleColname = "sample_id",
  scoreArcMinimum = 200,
  scoreFactor = 1,
  scoreArcFactor = 0.5,
  doStackJunctions = TRUE,
  strandedScore = TRUE,
  ref2c = NULL,
  verbose = FALSE,
  ...
)

Arguments

grl	GRangesList, or GRanges which will be converted to a GRangesList of length=1.
keepGRvalues, keepGRLvalues	logical indicating whether the output data.frame should include column values from GRangesList and GRanges, if available.
addGaps	logical indicating whether to add gap GRanges between same-strand GRanges features within each GRangesList element. When TRUE the gaps will be drawn between each GRanges rectangle.
width	numeric value of default width for features when shape="rectangle".
widthV	numeric vector whose names are column values, using values from the first available colname from width_colname. Some common defaults are provided. Values are suggested to be between 0 and 1, since each GRangesList element is separated by 1 y-axis unit.
width_colname	when widthV is used to determine width based upon a column value, the first matching colname of width_colname is used.
shape	character string indicating whether input data should be processed as rectangular segments or splice junction arcs.
scoreColname, scoreArcMinimum, scoreFactor, scoreArcFactor	numeric values used to determine junction ribbon height, the minimum height of the arc above the starting y-axis values based upon the score, the scaling factor for score values, and the relative height of the arc above the starting y-axis values multiplied by the score.
sampleColname	character string indicating the column containing biological sample identifier. This column is only used when type="junction", and when doStackJunctions=TRUE. It is used to ensure the junctions are only stacked within each sample. When sampleColname is not present in colnames(GenomicRanges::values(grl@unlistData)) then all junctions are stacked.
doStackJunctions	logical indicating whether to stack junctions at the start and end of junctions sharing the same coordinate, in order of shortest to longest junction width.
ref2c	optional output from make_ref2compressed() used to compress axis coordinates during junction arc calculations.
verbose	logical indicating whether to print verbose output.
...	additional arguments are passsed to relevant downstream functions.

Details

This function central to other plotting functions for GRanges and GRangesList objects. It currently has two modes:

• shape="rectangle" is intended for exons/peaks/regions, for example plotting exons in a gene structure, or plotting ChIP-seq peaks.

• shape="junction" is intended for splice junctions, and returns two polygons that join junction ends with a the middle point raised above both baselines. The polygon height is determined by the score, resulting in visual reinforcement of the number of splice junction reads, usually compared to the sequence read coverage at adjacent exons.

An interesting argument is baseline which can be a named vector of baseline y-axis values for each GRanges entry in the grl GRangesList object. For example, it can be used to shift exons up or down on the y-axis to make alternative exons more visibly distinct. When used for Sashimi plots, it should also be supplied to prepareSashimi() or exoncov2polygon() so the coverages and splice junctions have consistent y-axis baselines.

When chromosome coordinates are compressed (to reduce the visible width of introns) it affects the midpoint of splice junction arcs, therefore ref2c should be supplied so the arcs are defined using compresssed coordinates.

Value

data.frame with ⁠x,y⁠ coordinates, and id which is used to group polygon coordinates when used with ggplot2::geom_polygon() or ggforce::geom_shape(). When shape="rectangle" the colnames include grl_name which are names of the input GRangesList names(grl); gr_name which are names of the GRanges entries; and other columns from the input GRanges entries. When shape="junction" the data includes two polygons per junction, intended to be used with geom_diagonal_wide_arc() for each side in order to produce a ribbon arc. The data also includes sample_id which is helpful for keeping data distinct when derived from multiple samples.

See Also

Other jam GRanges functions: addGRLgaps(), addGRgaps(), annotateGRLfromGRL(), annotateGRfromGR(), assignGRLexonNames(), closestExonToJunctions(), combineGRcoverage(), exoncov2polygon(), findOverlapsGRL(), flattenExonsBy(), getFirstStrandedFromGRL(), getGRLgaps(), getGRcoverageFromBw(), getGRgaps(), jam_isDisjoint(), make_ref2compressed(), sortGRL(), spliceGR2junctionDF(), stackJunctions()

Other jam plot functions: bgaPlotly3d(), factor2label(), gene2gg(), jitter_norm(), plotSashimi(), prepareSashimi(), stackJunctions()

Other splicejam core functions: exoncov2polygon(), gene2gg(), make_ref2compressed(), plotSashimi(), prepareSashimi()

Examples

suppressPackageStartupMessages(library(GenomicRanges));
suppressPackageStartupMessages(library(jamba));
gr <- GenomicRanges::GRanges(seqnames=rep(c("chr1"), 7),
   ranges=IRanges::IRanges(start=c(50, 100, 1300, 2500, 23750, 24900, 25000),
      end=c(100, 150, 1450, 2600, 23800, 25000, 25200)),
   strand=rep("+", 7),
   feature_type=rep(c("noncds", "cds", "noncds"), c(1,5,1)));
names(gr) <- jamba::makeNames(rep("exon", 7));
grldf <- grl2df(gr, addGaps=TRUE);

gg1 <- ggplot2::ggplot(grldf, ggplot2::aes(x=x, y=y, group=id)) +
   ggforce::geom_shape(ggplot2::aes(fill=feature_type)) +
   colorjam::theme_jam()
print(gg1);

## For fun, compress the introns and plot again.
## This method uses x-axis breaks at the exon boundaries.
ref2c <- make_ref2compressed(gr);
gg2 <- gg1 +
   ggplot2::scale_x_continuous(trans=ref2c$trans_grc) +
   colorjam::theme_jam()
print(gg2);

## data can also be plotted using coord_trans()
## the main difference is that x-axis breaks are defined before the
## transformation, which can result in non-optimal placement
gg3 <- gg1 +
   ggplot2::coord_trans(x=ref2c$trans_grc) + colorjam::theme_jam();
print(gg3);

## An example showing splice junction data
data(test_junc_wide_gr);
junc_wide_df <- grl2df(test_junc_wide_gr, shape="junction");
ggWide1 <- ggplot2::ggplot(junc_wide_df,
   ggplot2::aes(x=x, y=y, group=gr_name, fill=gr_name, color=gr_name)) +
  splicejam::geom_diagonal_wide_arc() +
  colorjam::theme_jam() +
  colorjam::scale_fill_jam(alpha=0.7) +
  colorjam::scale_color_jam() +
  ggplot2::xlab("chr1") +
  ggplot2::ggtitle("junctions (full intron width)")
print(ggWide1);

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