Construct a Trace object from a Signac Object or Granges object

Problem 1: Signac objects and GRanges made from bigwigs are large and it is computationally expensive to get data from them when tweaking plots. Problem 2: For the most part we like how Signac plots genomic coverage of track-like data and we would like to show bulk data in a similar way with a similar compuatational interface. The trace object is a small intermediate object that holds the minimal amount of data you need to make a coverage plot showing accessibility or binding to a specific genomic region. Then you can use the trace object to quickly and easily generate tracks as needed for your plot. These tracks are all ggplots and are easy to configure for legible graphics using add-on layers. There are options for displaying groups by color or facet which are built in with good graphical defaults. If these are not suitable, they can be changed post hoc like any other ggplot.

Usage

bb_makeTrace(
  obj,
  gene_to_plot,
  genome = c("hg38", "danRer11"),
  extend_left = 0,
  extend_right = 0,
  peaks = NULL,
  bulk_group_col = "group",
  bulk_coverage_col = "coverage",
  fill_in = FALSE,
  fixed_width = 100
)

Arguments

obj: A Signac/Seurat object or a GRanges object. Import a bigwig file to a GRanges object using bb_import_bw to ensure proper formatting. Use plyranges functions to easily pre-filter the GRanges object e.g. by chr to reduce processing time. The precise range will be defined by gene_to_plot and the extend arguments. You may wish to add grouping metadata columns and to merge several bulk tracks. This can be done while importing using c(bw1, bw2).
gene_to_plot: The gene you want to display. Must be a valid gene in the genome assembly being used.
genome: The genome assembly. Required. Must be either "hg38" or "danRer11".
extend_left: Bases to extend plot_range left, or upstream relative to the top strand.
extend_right: Bases to extend plot_range right, or downstream relative to the top strand.
peaks: An optional GRanges object holding peak data. Ignored for Signac/Seurat objects which carry this internally.
bulk_group_col: Used only when making a Trace from a GRanges object. This identifies the metadata column holding the grouping information for the Trace data. It will be converted literally to "group" when the object is made. Recommendation is to import the bigwigs using import_bw which will set the group column and name it appropriately and then this can be left as the default. This is ignored for Signac/Seurat objects which report this by default in a column named group.
bulk_coverage_col: If you are making the object from a bigwig/GRanges, you need to identify which column in your bigwig/GRanges object holds the coverage data to plot on the y axis. Defaults to "coverage". Similar to bulk_group_col, if you import the bigwig using bb_import_bw, it should already be named appropriately. Will be ignored for Signac/Seurat objects which use "coverage" by default.
fill_in: Some track data may be very sparse. This probably depends on how it was generated. It seems that nextflow bigwigs have missing data where there is no signal but data from Signac is more complete with zeros. The problem with missing data is that it makes the line plot look jagged. This option allows you to fill in gaps in the trace data with 0's. This is done by tiling the regions without real signal, leaving the ranges with real signal untouched. Default is FALSE for compatibility with older code. TRUE will fill in the gaps.
fixed_width: Bin width for filling in gaps in sparse genome track data. Defaults to 100 bp.