SingleCoveragePlot: Plot Tn5 insertion sites over a region

Description

Plot fragment coverage (frequence of Tn5 insertion) within given regions for groups of cells.

Usage

SingleCoveragePlot(
  object,
  region,
  annotation = NULL,
  ucsc = TRUE,
  peaks = NULL,
  assay = NULL,
  fragment.path = NULL,
  group.by = NULL,
  window = 100,
  downsample = 0.1,
  height.tracks = 10,
  extend.upstream = 0,
  extend.downstream = 0,
  ymax = NULL,
  scale.factor = NULL,
  cells = NULL,
  idents = NULL,
  sep = c("-", "-")
)
CoveragePlot(
  object,
  region,
  annotation = NULL,
  ucsc = TRUE,
  peaks = NULL,
  assay = NULL,
  fragment.path = NULL,
  group.by = NULL,
  window = 100,
  downsample = 0.1,
  height.tracks = 10,
  extend.upstream = 0,
  extend.downstream = 0,
  scale.factor = NULL,
  ymax = NULL,
  cells = NULL,
  idents = NULL,
  sep = c("-", "-"),
  ...
)

Arguments

object

A Seurat object

region

A set of genomic coordinates to show. Can be a GRanges object, a string, or a vector of strings describing the genomic coordinates to plot.

annotation

An Ensembl based annotation package

ucsc

Set annotation seqlevels style to UCSC

peaks

A GRanges object containing peak coordinates

assay

Name of the assay to plot

fragment.path

Path to an index fragment file. If NULL, will look for a path stored for the requested assay using the SetFragments function

group.by

Name of one or more metadata columns to group (color) the cells by. Default is the current cell identities

window

Smoothing window size

downsample

Fraction of positions to retain in the plot. Default is 0.1 (retain 10 percent, ie every 10th position)

height.tracks

Height of the accessibility tracks relative to the height of the gene annotation track. Default is 2 (twice as high as annotation track).

extend.upstream

Number of bases to extend the region upstream (Default 0)

extend.downstream

Number of bases to extend the region downstream (Default 0)

ymax

Maximum value for Y axis. If NULL (default) set to the highest value among all the tracks.

scale.factor

Scaling factor for track height. If NULL (default), use the median group scaling factor determined by total number of fragments sequences in each group.

cells

Which cells to plot. Default all cells

idents

Which identities to include in the plot. Default is all identities.

sep

Separators to use for strings encoding genomic coordinates. First element is used to separate the chromosome from the coordinates, second element is used to separate the start from end coordinate.

...

Additional arguments passed to wrap_plots

Value

Returns a ggplot object

Details

Thanks to Andrew Hill for providing an early version of this function http://andrewjohnhill.com/blog/2019/04/12/streamlining-scatac-seq-visualization-and-analysis/

Examples

Run this code

# NOT RUN {
fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
atac_small <- SetFragments(atac_small, file = fpath)
CoveragePlot(object = atac_small, region = c("chr1-713500-714500"))
# }

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