plot_genome_track: Plot genome tracks in linear or circular layout

In TmCalculator: Genome-Wide Nucleic Acid Melting Temperature Profiling and Multi-Omics Integration

Plot genome tracks in linear or circular layout

Description

Visualise genomic tracks as either a linear karyoploteR plot or a circular plot (base R graphics). Set circular = TRUE to switch to the circular layout; the same track_list works for both views without modification.

Supported track types in each list element:

• type = "rect" : data as GRanges/data.frame, drawn as rectangles

• type = "line" : data as GRanges/data.frame with value_col, drawn as lines

• type = "area" : same as line but filled (linear only)

• type = "region": piled-up regions (linear only)

• type = "coverage": coverage area plot (linear only)

A track with ideogram = TRUE is drawn inside the chromosome bar (linear) or as the outermost ring with a grey background (circular). Only "rect" type is supported for ideogram tracks.

A per-track height field (numeric, default 1) controls relative sizing. In linear mode heights are proportional fractions of the data panel; in circular mode they scale the radial thickness of each ring.

A per-track highlight field (list or list-of-lists with data/col/alpha/border) draws highlight bands within that track only.

Entries with type = "highlight" draw translucent bands spanning all real tracks. These accept: data, col (default "#F1C40F"), alpha (default 0.18), border (default NA), and min.degree (circular only, default 0.4).

Each list element may also contain: name, col, bg.col, border, ylim, lwd, alpha (0–1 transparency), legend_font_col, ideogram, height, highlight.

Usage

plot_genome_track(
  genome_name,
  genome_size = NULL,
  genome = NULL,
  track_list,
  circular = FALSE,
  label = NULL,
  chromosomes = NULL,
  zoom = NULL,
  plot.type = 1,
  track.gap = 0.01,
  legend.show = TRUE,
  legend.position = NULL,
  legend.cex = 0.6,
  legend.bty = "n",
  legend.border = NA,
  legend.font.col = "black",
  legend.lwd = 1,
  legend.seg.len = -0.5,
  legend.box.lwd = 0.25,
  legend.x.intersp = 1,
  legend.lty = 1,
  axis.cex = NULL,
  title.cex = NULL,
  base.tick.dist = NULL,
  start.degree = 34.47,
  track.height = 0.05,
  gap.after = 0,
  cell.padding = c(0, 0, 0, 0),
  track.margin = c(0.005, 0.005),
  circle.margin = c(0.001, 0.001),
  canvas.xlim = c(-1, 1),
  canvas.ylim = c(-1, 1),
  axis.unit = "Mb",
  axis.step = NULL,
  axis.show.unit = FALSE,
  label.column = 4,
  label.niceFacing = TRUE,
  label.cex = 0.6,
  label.side = "inside",
  label.labels_height = 0.01,
  label.connection_height = 0.03,
  label.line_lwd = 0.25
)

Arguments

genome_name	Character. Used for the title.
genome_size	Numeric. Total genome length (single-chromosome genomes).
genome	Optional GRanges, or a karyoploteR genome string (e.g. "hg38"). Ignored in circular mode.
track_list	List of track specs (see above).
circular	Logical. If TRUE, render as a circular plot using base R graphics instead of a karyoploteR linear plot.
label	Optional data.frame/GRanges with labels.
chromosomes	Character vector to restrict/reorder chromosomes (linear only).
zoom	A GRanges object, a character string, or a character vector specifying one or more regions to zoom into (e.g. "chr1:1e6-2e6" or c("chr1:1e6-1.2e6", "chr1:3e6-3.2e6")). In linear mode each region is drawn as a separate stacked panel. In circular mode the regions are concatenated around the circle with small gaps between them. NULL (default) shows the full genome.
plot.type	karyoploteR plot.type (linear only).
track.gap	Relative gap between tracks (linear only, 0 to ~0.05).
legend.show	Logical.
legend.position	Legend position. Character for linear (e.g. "topright"), numeric vector of length 2 for circular (e.g. c(0.75, 1)).
legend.cex, legend.bty, legend.border	See legend.
legend.font.col	Character. Default legend text colour.
legend.lwd, legend.seg.len, legend.box.lwd, legend.x.intersp, legend.lty	Additional legend parameters.
axis.cex	Axis label size.
title.cex	Title size.
base.tick.dist	Numeric or NULL (linear only).
start.degree	Numeric. Starting angle in degrees for the circular layout (default 34.47, matching the circlize convention).
track.height, gap.after, cell.padding, track.margin	Kept for backward compatibility; ignored in the base R circular layout.
circle.margin	Numeric vector (length 2 or 4) controlling plot margins as fractions of the device size. Length 2 is recycled as c(bottom, left, bottom, left). Default c(0.001, 0.001).
canvas.xlim, canvas.ylim	Numeric length-2 vectors controlling the plotting window (circular only). Adjust to pan or zoom into a portion of the circle.
axis.unit, axis.step, axis.show.unit	Circular axis parameters.
label.column, label.niceFacing, label.cex, label.side, label.labels_height, label.connection_height, label.line_lwd	Circular label parameters.

Value

Invisibly returns the KaryoPlot object (linear) or NULL (circular).

Examples

## Not run: 
data(ecoli_rep_hotspots)

library("BSgenome.Ecoli.NCBI.ASM584v2")
genome_name <- "BSgenome.Ecoli.NCBI.ASM584v2"
chr_name    <- "U00096.3"
genome <- get(genome_name, envir = asNamespace(genome_name))
chr_length  <- length(genome[[chr_name]])
genome_name="BSgenome.Ecoli.NCBI.ASM584v2"
bins_gc <- make_genomiccoord(
  bsgenome    = genome_name,
  chromosomes = chr_name,
  window      = 200L,
  slide       = 200L,
  start       = 1,
  end         = chr_length,
  strand      = "+"
)
input_new <- list(pkg_name = genome_name, seq = bins_gc)
gr_batch <- to_genomic_ranges_fast(input_new)
tm_ASM584v2 <- tm_calculate(
  gr_batch,
  method   = "tm_nn"
)
Tm <- as.data.frame(tm_ASM584v2$gr[, c("Tm", "GC")])

tracks <- list(
  list(type = "rect", data = ecoli_rep_hotspots$all_peaks_IP_mutH,
       col = "#2C3E50", bg.col = "grey", name = "MutL-AR",
       legend_font_col = "#2C3E50", ideogram = TRUE, height = 0.5),
  list(type = "line", data = Tm, value_col = "GC",
       name = "GC content", col = "#4A90E2",
       legend_font_col = "#4A90E2"),
  list(type = "line", data = Tm, value_col = "Tm",
       name = "Melting temp", col = "#E06666",
       legend_font_col = "#E06666", height = 2),
  list(type = "line", data = ecoli_rep_hotspots$bins_rep,
       value_col = "count", name = "Microsatellites", col = "#2ECC71",
       legend_font_col = "#2ECC71"),
  list(type = "line", data = ecoli_rep_hotspots$bins_cru,
       value_col = "count", name = "Cruciform", col = "#3B3E6B",
       legend_font_col = "#3B3E6B"),
  list(data = ecoli_rep_hotspots$ssdna, name = "ssDNA",
       col = "#8E44AD", legend_font_col = "#8E44AD"),
  list(type = "line", data = ecoli_rep_hotspots$bins_gatc,
       value_col = "count", name = "GATC sites", col = "#D35400",
       legend_font_col = "#D35400"),
  list(type = "highlight", data = ecoli_rep_hotspots$all_peaks_IP_mutH,
       col = "#F1C40F", alpha = 0.18)
)

# Circular
plot_genome_track("E. coli", genome_size = 4641652,
                  track_list = tracks, circular = TRUE)

# Linear
plot_genome_track("E. coli", genome_size = 4641652,
                  track_list = tracks)

# Linear zoom (single region)
plot_genome_track("E. coli", genome_size = 4641652,
                  track_list = tracks,
                  zoom = "U00096.3:1000000-2000000")

# Linear zoom (multiple regions — stacked panels)
plot_genome_track("E. coli", genome_size = 4641652,
                  track_list = tracks,
                  zoom = c("U00096.3:1000000-1200000",
                           "U00096.3:3000000-3200000"))

# Circular zoom (multiple regions — concatenated arcs)
plot_genome_track("E. coli", genome_size = 4641652,
                  track_list = tracks, circular = TRUE,
                  zoom = c("U00096.3:1000000-1200000",
                           "U00096.3:3000000-3200000"))

# Circular with canvas panning
plot_genome_track("E. coli", genome_size = 4641652,
                  track_list = tracks, circular = TRUE,
                  canvas.xlim = c(0.5, 1), canvas.ylim = c(0, 1),
                  circle.margin = c(0.05, 0.05))

## End(Not run)

TmCalculator documentation built on Aug. 28, 2026, 5:09 p.m.