SV Plotting Functions

API reference for structural variant visualization

1 SV Plotting Functions

Note

This reference is curated against the current app/logic/plot_sv.R implementation. The primary plotting entry point is sv_plotly() (not plot_sv_tracks()).

1.1 Overview

The plot_sv.R module provides visualization for structural variants in the IMPACT Plot. SVs are displayed as horizontal segments positioned by genomic coordinates, separated by SV type along the y-axis.

Location: app/logic/plot_sv.R

1.2 Key Functions

1.2.1 sv_plotly()

Builds the SV plot as a plotly widget from an AnnotSV TSV file path.

Parameters: - sv_path (character|NULL): Path to SV TSV file. If missing/invalid, returns baseline_sv_plotly(). - selected_chr (character): "All" or chromosome string. - variant_states (list|data.frame|NULL): Optional per-variant annotations keyed by AnnotSV_ID (or SV_<AnnotSV_ID>). - show_failed_qc (logical): If FALSE, filters out SVs failing READ_SUPPORT_FILTERING. - acmg_filter (character|NULL): Optional subset of allowed ACMG_class values. - sv_genotype (character|NULL): Optional allowed genotype set (normalized to 0/1, 1/1, etc.).

Returns: plotly object

Details: - Coordinates are computed in Mb; in genome-wide mode, cumulative chromosome offsets from plot_gds$chr_lengths() are applied. - Y-axis categories are SV types (Deletion/Duplication/Insertion/Inversion/Translocation). - Point shape is derived from genotype (diamond for 1/1, otherwise circle) when genotype fields are available.

1.3 Usage

box::use(
  app/logic/plot_sv[sv_plotly]
)

# Create SV panel for IMPACT Plot
p <- sv_plotly(
  sv_path = "app/data/sample_1_SV_IMPACT.tsv",
  selected_chr = "All",
  show_failed_qc = FALSE
)

1.4 Supporting helpers (exported)

  • sv_colors(): named vector mapping SV types to colors.
  • baseline_sv_plot() / baseline_sv_plotly(): empty placeholders used when no data is available.
  • load_sv_data(sv_path): permissive file reader + light AnnotSV column normalization used internally by sv_plotly().

1.5 Interactivity

All plots return plotly objects with hover tooltips, zoom, and pan capabilities: - Hover Tooltips: View detailed SV annotations (type, coordinates, genes affected, etc.) - Zoom/Pan: Synchronized with other IMPACT Plot panels - Track Separation: Five distinct horizontal tracks prevent visual overlap

1.6 See Also