CoveragePlot: Plot Tn5 insertion frequency over a region

In timoast/signac: Analysis of Single-Cell Chromatin Data

Plot Tn5 insertion frequency over a region

Description

Plot frequency of Tn5 insertion events for different groups of cells within given regions of the genome. Tracks are normalized using a per-group scaling factor computed as the number of cells in the group multiplied by the mean sequencing depth for that group of cells. This accounts for differences in number of cells and potential differences in sequencing depth between groups.

Usage

CoveragePlot(
  object,
  region,
  features = NULL,
  assay = NULL,
  split.assays = FALSE,
  assay.scale = "common",
  show.bulk = FALSE,
  expression.assay = "RNA",
  expression.slot = "data",
  annotation = TRUE,
  peaks = TRUE,
  peaks.group.by = NULL,
  ranges = NULL,
  ranges.group.by = NULL,
  ranges.title = "Ranges",
  region.highlight = NULL,
  links = TRUE,
  tile = FALSE,
  tile.size = 100,
  tile.cells = 100,
  bigwig = NULL,
  bigwig.type = "coverage",
  bigwig.scale = "common",
  heights = NULL,
  group.by = NULL,
  split.by = NULL,
  window = 100,
  extend.upstream = 0,
  extend.downstream = 0,
  scale.factor = NULL,
  ymax = NULL,
  cells = NULL,
  idents = NULL,
  sep = c("-", "-"),
  max.downsample = 3000,
  downsample.rate = 0.1,
  ...
)

Arguments

object	A Seurat object
region	A set of genomic coordinates to show. Can be a GRanges object, a string encoding a genomic position, a gene name, or a vector of strings describing the genomic coordinates or gene names to plot. If a gene name is supplied, annotations must be present in the assay.
features	A vector of features present in another assay to plot alongside accessibility tracks (for example, gene names).
assay	Name of the assay to plot. If a list of assays is provided, data from each assay will be shown overlaid on each track. The first assay in the list will define the assay used for gene annotations, links, and peaks (if shown). The order of assays given defines the plotting order.
split.assays	When plotting data from multiple assays, display each assay as a separate track. If FALSE, data from different assays are overlaid on a single track with transparancy applied.
assay.scale	Scaling to apply to data from different assays. Can be: common: plot all assays on a common scale (default) separate: plot each assay on a separate scale ranging from zero to the maximum value for that assay within the plotted region
show.bulk	Include coverage track for all cells combined (pseudo-bulk). Note that this will plot the combined accessibility for all cells included in the plot (rather than all cells in the object).
expression.assay	Name of the assay containing expression data to plot alongside accessibility tracks. Only needed if supplying features argument.
expression.slot	Name of slot to pull expression data from. Only needed if supplying the features argument.
annotation	Display gene annotations. Set to TRUE or FALSE to control whether genes models are displayed, or choose "transcript" to display all transcript isoforms, or "gene" to display gene models only (same as setting TRUE).
peaks	Display peaks
peaks.group.by	Grouping variable to color peaks by. Must be a variable present in the feature metadata. If NULL, do not color peaks by any variable.
ranges	Additional genomic ranges to plot
ranges.group.by	Grouping variable to color ranges by. Must be a variable present in the metadata stored in the ranges genomic ranges. If NULL, do not color by any variable.
ranges.title	Y-axis title for ranges track. Only relevant if ranges parameter is set.
region.highlight	Region to highlight on the plot. Should be a GRanges object containing the coordinates to highlight. By default, regions will be highlighted in grey. To change the color of the highlighting, include a metadata column in the GRanges object named "color" containing the color to use for each region.
links	Display links. This can be a TRUE/FALSE value which will determine whether a links track is displayed, and if TRUE links for all genes in the plotted region will be shown. Alternatively, a character vector can be provided, giving a list of gene names to plot links for. If this is provided, only links for those genes will be displayed in the plot.
tile	Display per-cell fragment information in sliding windows. If plotting multi-assay data, only the first assay is shown in the tile plot.
tile.size	Size of the sliding window for per-cell fragment tile plot
tile.cells	Number of cells to display fragment information for in tile plot.
bigwig	List of bigWig file paths to plot data from. Files can be remotely hosted. The name of each element in the list will determine the y-axis label given to the track.
bigwig.type	Type of track to use for bigWig files ("line", "heatmap", or "coverage"). Should either be a single value, or a list of values giving the type for each individual track in the provided list of bigwig files.
bigwig.scale	Same as assay.scale parameter, except for bigWig files when plotted with bigwig.type="coverage"
heights	Relative heights for each track (accessibility, gene annotations, peaks, links).
group.by	Name of one or more metadata columns to group (color) the cells by. Default is the current cell identities
split.by	A metadata variable to split the tracks by. For example, grouping by "celltype" and splitting by "batch" will create separate tracks for each combination of celltype and batch.
window	Smoothing window size
extend.upstream	Number of bases to extend the region upstream.
extend.downstream	Number of bases to extend the region downstream.
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.
ymax	Maximum value for Y axis. Can be one of: NULL: set to the highest value among all the tracks (default) qXX: clip the maximum value to the XX quantile (for example, q95 will set the maximum value to 95% of the maximum value in the data). This can help remove the effect of extreme values that may otherwise distort the scale. numeric: manually define a Y-axis limit
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.
max.downsample	Minimum number of positions kept when downsampling. Downsampling rate is adaptive to the window size, but this parameter will set the minimum possible number of positions to include so that plots do not become too sparse when the window size is small.
downsample.rate	Fraction of positions to retain when downsampling. Retaining more positions can give a higher-resolution plot but can make the number of points large, resulting in larger file sizes when saving the plot and a longer period of time needed to draw the plot.
...	Additional arguments passed to wrap_plots

Details

Additional information can be layered on the coverage plot by setting several different options in the CoveragePlot function. This includes showing:

• gene annotations

• peak positions

• additional genomic ranges

• additional data stored in a bigWig file, which may be hosted remotely

• gene or protein expression data alongside coverage tracks

• peak-gene links

• the position of individual sequenced fragments as a heatmap

• data for multiple chromatin assays simultaneously

• a pseudobulk for all cells combined

Value

Returns a patchwork object

Examples

fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
fragments <- CreateFragmentObject(
  path = fpath,
  cells = colnames(atac_small),
  validate.fragments = FALSE
)
Fragments(atac_small) <- fragments

# Basic coverage plot
CoveragePlot(object = atac_small, region = c("chr1-713500-714500"))

# Show additional ranges
ranges.show <- StringToGRanges("chr1-713750-714000")
CoveragePlot(object = atac_small, region = c("chr1-713500-714500"), ranges = ranges.show)

# Highlight region
CoveragePlot(object = atac_small, region = c("chr1-713500-714500"), region.highlight = ranges.show)

# Change highlight color
ranges.show$color <- "orange"
CoveragePlot(object = atac_small, region = c("chr1-713500-714500"), region.highlight = ranges.show)

# Show expression data
CoveragePlot(object = atac_small, region = c("chr1-713500-714500"), features = "ELK1")

timoast/signac documentation built on Aug. 23, 2024, 1:48 a.m.