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Multi-track genomic visualization (base R graphics)

Source: R/plot_tracks_fast.R
plot_tracks.Rd

Renders a stacked multi-panel genome browser view using base R graphics. Includes gene model, BigWig signal tracks (ATAC, RNA, histone), enhancer index, chromatin state bars, FANTOM/UCNE annotations, TF binding peaks, and ncRNA annotations. A translucent violet highlight column marks the enhancer region of interest across all panels. Typically renders in 1-2 seconds.

Usage

plot_tracks(
  putative_enhanceosome,
  index,
  database,
  track_connection,
  keep_epitracks = TRUE,
  chromatin_states = NULL,
  gene_lookup = FALSE,
  show_bigwig = TRUE,
  show_chromatin = TRUE,
  show_annotations = TRUE,
  show_gene_model = TRUE,
  show_enhancer_highlight = TRUE,
  mirror = TRUE,
  signal_style = c("line", "polygon"),
  signal_layout = "auto",
  cex_cell_label = 1.4,
  cex_axis = 1.2,
  cex_coord = 1.3,
  cex_annotation = 1.1,
  cex_gene = 1.2,
  cex_title = 1.5,
  cex_signal_label = 1.2,
  quantile_cap = 0.98,
  scale_factor = 1.1,
  export = NULL,
  width = 10,
  height = 8
)

plot_tracks_fast(
  putative_enhanceosome,
  index,
  database,
  track_connection,
  keep_epitracks = TRUE,
  chromatin_states = NULL,
  gene_lookup = FALSE,
  show_bigwig = TRUE,
  show_chromatin = TRUE,
  show_annotations = TRUE,
  show_gene_model = TRUE,
  show_enhancer_highlight = TRUE,
  mirror = TRUE,
  signal_style = c("line", "polygon"),
  signal_layout = "auto",
  cex_cell_label = 1.4,
  cex_axis = 1.2,
  cex_coord = 1.3,
  cex_annotation = 1.1,
  cex_gene = 1.2,
  cex_title = 1.5,
  cex_signal_label = 1.2,
  quantile_cap = 0.98,
  scale_factor = 1.1,
  export = NULL,
  width = 10,
  height = 8
)

Arguments

putative_enhanceosome

epiRomics class database containing putative enhanceosome calls

index

numeric of row value from putative_enhanceosome to visualize

database

epiRomics class database containing all data initially loaded

track_connection

data frame containing bigwig track locations and their names

keep_epitracks

logical indicating whether to show enhancer and chip tracks, default is TRUE

chromatin_states

data.frame, optional output from classify_chromatin_states. When provided, the enhancer track is colored by chromatin state and separate per-state annotation tracks are added.

gene_lookup

logical. When TRUE, omits the enhancer index bar and violet highlight column. Used internally by plot_gene_tracks to display a gene locus without enhancer-specific visual elements. Default is FALSE.

show_bigwig

logical. Show BigWig signal tracks. Default TRUE.

show_chromatin

logical. Show chromatin state color tracks. Default TRUE.

show_annotations

logical. Show BED annotation tracks. Default TRUE.

show_gene_model

logical. Show gene model panel. Default TRUE.

show_enhancer_highlight

logical. Show enhancer index highlight. Default TRUE.

mirror

logical. Use symmetric mirrored axes for paired ATAC/RNA signals. Default TRUE.

signal_style

character. Signal rendering style: "line" (default) draws vertical bars at each position (IGV/UCSC browser style), "polygon" draws filled area charts.

signal_layout

character. Signal rendering layout: "auto" detects paired signals and mirrors, "stacked" renders one row per signal, "mirrored" always mirrors first two. Default "auto".

cex_cell_label

numeric. Font size for cell type labels (e.g. Alpha, Beta). Default 1.4.

cex_axis

numeric. Font size for y-axis tick labels on signal tracks. Default 1.2.

cex_coord

numeric. Font size for chromosome, start, stop, genome build text. Default 1.3.

cex_annotation

numeric. Font size for BED annotation labels. Default 1.1.

cex_gene

numeric. Font size for gene name labels in gene model. Default 1.2.

cex_title

numeric. Font size for main plot title. Default 1.5.

cex_signal_label

numeric. Font size for ATAC/RNA type indicator text. Default 1.2.

quantile_cap

numeric. Percentile for capping extreme signal peaks (default 0.98). Peaks above this percentile are clipped to prevent axis compression.

scale_factor

numeric. Y-axis headroom multiplier (default 1.1). Values above 1.0 add whitespace above the tallest signal peak.

export

character or NULL. File path to auto-export the plot (e.g. "plot.pdf", "plot.eps", "plot.png"). When NULL (default), plot is drawn on current device only.

width

numeric. Export width in inches. Default 10.

height

numeric. Export height in inches. Default 8.

Value

Invisible NULL. The function produces a base R multi-panel plot on the current graphics device.

Examples

## plot_tracks requires a TxDb (Suggests) and a real BigWig file.
## This example confirms input validation fires correctly.
db <- make_example_database()
eso <- make_example_enhanceosome(db)
tc  <- data.frame(path = character(), name = character(),
  color = character(), type = character(),
  stringsAsFactors = FALSE)
if (requireNamespace("TxDb.Hsapiens.UCSC.hg38.knownGene", quietly = TRUE)) {
  tryCatch(
    plot_tracks(eso, 1L, db, tc),
    error = function(e) message(e$message)
  )
}
#>   2169 genes were dropped because they have exons located on both strands of
#>   the same reference sequence or on more than one reference sequence, so cannot
#>   be represented by a single genomic range.
#>   Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList
#>   object, or use suppressMessages() to suppress this message.