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Easy sashimi plot visualization

Source: R/ez_wrappers.R
ez_sashimi.Rd

This function creates a sashimi plot combining coverage tracks with splice junction arcs. It is commonly used for RNA-seq data to visualize both read coverage and splicing events. Supports the same flexible input types as ez_coverage.

Usage

ez_sashimi(
  coverage_data,
  junction_data,
  region,
  track_labels = NULL,
  colors = "purple3",
  coverage_fill = NULL,
  junction_direction = c("alternate", "up", "down"),
  junction_curvature = 0.05,
  height_factor = 0.05,
  alpha = 1,
  score_transform = c("identity", "log10", "sqrt"),
  linewidth_range = c(0.1, 1.5),
  show_labels = TRUE,
  label_size = 3,
  label_color = "black",
  y_axis_style = c("none", "simple", "full"),
  facet_label_position = c("top", "left"),
  border = FALSE,
  show_legend = FALSE,
  ...
)

Arguments

coverage_data

Coverage input: a GRanges object, data frame, character vector of file paths, or named list of data sources. Same input types as ez_coverage. When a named list is provided, each element becomes a separate faceted track.

junction_data

Junction input that must match the structure of coverage_data:

  • If coverage_data is a single source (GRanges, data.frame, or file path), junction_data must also be a single source.

  • If coverage_data is a named list, junction_data must be a named list with the same names.

region

Genomic region to display (e.g., "chr1:1000000-2000000")

track_labels

Optional vector of track labels (used for unnamed list input)

colors

Color(s) for coverage fill and junction arcs. Can be a single color or a vector of colors for multiple tracks. If fewer colors than tracks are provided, colors will be recycled. Default: "purple3"

coverage_fill

Deprecated. Use colors instead.

junction_direction

Direction of junction arcs: "alternate" (default, odd junctions up, even down), "up" (all arcs above coverage), or "down" (all arcs below zero line)

junction_curvature

Curvature of junction arcs (0-1). Higher values create more pronounced curves. Default: 0.05

height_factor

Height of arcs as proportion of genomic distance span. Higher values create taller arcs. Default: 0.05

alpha

Transparency for both coverage and junction arcs (0-1). Default: 1

score_transform

Transformation for junction scores when mapping to line width: "identity" (no transformation), "log10", or "sqrt". Default: "identity"

linewidth_range

Range of line widths for junction arcs, mapped from score. Default: c(0.1, 1.5)

show_labels

Logical, whether to show score labels at arc centers. Default: TRUE

label_size

Font size for score labels. Default: 3

label_color

Color for score labels. Default: "black"

y_axis_style

Y-axis style: "none", "simple", or "full". Default: "none"

facet_label_position

Position of facet labels: "top" or "left" (default: "top"). Only applies when using multiple tracks via named list input.

border

Logical. If TRUE, adds a black border around the plotting panel (default: FALSE)

show_legend

Logical. If TRUE, displays the legend (default: FALSE)

...

Additional arguments passed to geom_coverage

Value

A ggplot2 object representing the sashimi plot

Details

Sashimi plots combine two visual elements:

  • Coverage track: Shows read depth across the region as a filled area

  • Junction arcs: Connect splice donor and acceptor sites, with line width proportional to the number of supporting reads (score)

For "up" direction, arc endpoints are positioned at the coverage height at those positions. For "down" direction, arcs extend below the zero line. The "alternate" mode assigns alternating directions to junctions sorted by start position, which helps reduce visual overlap.

Junction scores are mapped to line width using the specified transformation. Use "log10" or "sqrt" for data with wide score ranges to prevent very thick lines.

For multi-track visualization, provide named lists for both coverage_data and junction_data with matching names. Each track will be displayed as a separate facet with its own coverage and junction arcs.

Examples

# Basic sashimi plot
coverage <- data.frame(
  seqnames = "chr1", start = 1:100, end = 2:101,
  score = c(runif(30, 5, 10), rep(0, 20), runif(50, 5, 10))
)
junctions <- data.frame(
  seqnames = "chr1", start = c(30), end = c(50), score = c(15)
)
ez_sashimi(coverage, junctions, "chr1:1-100")


# Multi-track sashimi plot with named lists
cov_list <- list("Sample1" = coverage1, "Sample2" = coverage2)
#> Error: object 'coverage1' not found
junc_list <- list("Sample1" = junctions1, "Sample2" = junctions2)
#> Error: object 'junctions1' not found
ez_sashimi(cov_list, junc_list, "chr1:1-100", colors = c("purple", "orange"))
#> Error: object 'cov_list' not found