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Draw gene models

Source: R/seq_gene.R
seq_gene.Rd

Composite element rendering gene models with backbone lines, exon/UTR boxes, directional arrows, and labels. Entirely format-agnostic — supply the relevant column names via map().

Usage

seq_gene(
  data = NULL,
  mapping = NULL,
  aesthetics = aes(),
  backbone_type = "arrow",
  show_start = FALSE,
  tss_position = NULL,
  separate_strands = FALSE,
  style_type = c("exon", "gene", "point"),
  ...
)

Arguments

data

Optional GRanges.

mapping

Optional SeqMap. Recognised fields: group (feature-to-gene grouping; features sharing a value are one gene), strand (default "+"), label (defaults to the group value), type ("exon" full-height box, "UTR" 80-percent-height box, anything else no box), and color (per-feature color).

aesthetics

Optional SeqAes. Supports color (default "gray30"), linewidth, alpha.

backbone_type

Character. One of "arrow" (default), "solid", or "dashed". Controls backbone line style and whether chevron arrows are drawn. Ignored when style_type is "gene" or "point" (no backbone exists in those modes).

show_start

Logical. When TRUE, a TSS flag arrow is drawn above the first exon of each gene. Default FALSE. Ignored when style_type = "point" (the point itself marks the TSS).

tss_position

Named list overriding per-gene TSS genomic positions. Keys are gene IDs; values are c(start, end) genomic coordinates. Default NULL (auto-detected from first exon by row order).

separate_strands

Logical. When TRUE, genes are split into "+" (top) and "-" (bottom) sub-bands, each labelled. Silently ignored when only one strand is present. Default FALSE.

style_type

Character. One of "exon" (default), "gene", or "point". Selects the per-gene rendering style: "exon" draws the full backbone with exon/UTR boxes; "gene" draws a single chevron-shaped polygon spanning the gene extent (no exon detail); "point" draws a single filled circle at the TSS. Labels are drawn in all three modes.

...

Additional arguments reserved for future use.

Value

A SeqGeneR6 instance.

Examples

seq_gene(map(group = gene_id, strand = strand, label = gene_name))
#> <SeqGene>
#>   Inherits from: <SeqElement>
#>   Public:
#>     .infer_scale_y: function () 
#>     aesthetics: SeqAes
#>     auto_legend: NULL
#>     backbone_type: arrow
#>     clone: function (deep = FALSE) 
#>     collect_legend_keys: function () 
#>     coordCanvas: NULL
#>     data: NULL
#>     draw: function () 
#>     exon_height: 0.8
#>     initialize: function (data = NULL, mapping = NULL, aesthetics = aes(), backbone_type = "arrow", 
#>     label_cex: 0.6
#>     label_offset: 0.01
#>     label_pad: 50000
#>     legend: NULL
#>     mapping: SeqMap
#>     prep: function (layout_track, track_windows) 
#>     resolve: function (track_data = NULL, track_mapping = NULL) 
#>     resolved: NULL
#>     separate_strands: FALSE
#>     show_legend: TRUE
#>     show_start: FALSE
#>     style_type: exon
#>     tss_position: NULL