Pseudobulk coverage trackplot

Plot a pseudobulk genome track, showing the number of fragment insertions across a region for each cell type or group.

Usage

trackplot_coverage(
  fragments,
  region,
  groups,
  cell_read_counts,
  group_order = NULL,
  bins = 500,
  clip_quantile = 0.999,
  colors = discrete_palette("stallion"),
  legend_label = NULL,
  zero_based_coords = !is(region, "GRanges"),
  return_data = FALSE
)

Arguments

fragments: Fragments object
region: Region to plot, e.g. output from gene_region(). String of format "chr1:100-200", or list/data.frame/GRanges of length 1 specifying chr, start, end. See help("genomic-ranges-like") for details
groups: Vector with one entry per cell, specifying the cell's group
cell_read_counts: Numeric vector of read counts for each cell (used for normalization)
group_order: Optional vector listing ordering of groups
bins: Number of bins to plot across the region
clip_quantile: (optional) Quantile of values for clipping y-axis limits. Default of 0.999 will crop out just the most extreme outliers across the region. NULL to disable clipping
colors: Character vector of color values (optionally named by group)
legend_label: Custom label to put on the legend (no longer used as color legend is not shown anymore)
zero_based_coords: Whether to convert the ranges from a 1-based end-inclusive coordinate system to a 0-based end-exclusive coordinate system. Defaults to true for GRanges and false for other formats (see this archived UCSC blogpost)
return_data: If true, return data from just before plotting rather than a plot.
scale_bar: Whether to include a scale bar in the top track (TRUE or FALSE)

Value

Returns a combined plot of pseudobulk genome tracks. For compatability with draw_trackplot_grid(), the extra attribute $patches$labels will be added to specify the labels for each track. If return_data or return_plot_list is TRUE, the return value will be modified accordingly.

Usage

Arguments

Value

See also