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IGV-style read alignment track element

Source: R/seq_reads.R
seq_reads.Rd

Renders read alignments from an indexed BAM file as chevron polygons (pointing right for + strand reads, left for −). Mate pairs are optionally connected by a thin horizontal line. Reads are loaded once at construction time and cached on the element; only the requested windows are pulled.

Usage

seq_reads(
  bam,
  region,
  min_mapq = 0L,
  max_reads = 20000L,
  max_width = 100000L,
  sort_by = c("insert_length", "start"),
  link_mates = TRUE,
  show_strand = TRUE,
  aesthetics = list()
)

Arguments

bam

Character. Path to an indexed BAM file.

region

GRanges of windows to load. Every window must be ≤ max_width bp.

min_mapq

Integer. Minimum mapping quality. Default 0.

max_reads

Integer. Maximum total reads to load (qname-aware downsampling preserves mate pairs). Default 20000.

max_width

Integer. Maximum allowed window width in bp. Default 100000. Prevents accidental loading of entire chromosomes.

sort_by

Character. Row-packing sort order: "insert_length" (default — longest inserts at the top) or "start" (leftmost reads at the top).

Logical. Draw a horizontal line connecting each mated pair's outer extent. Default TRUE.

show_strand

Logical. Draw chevron arrowheads indicating strand. Default TRUE.

aesthetics

Named list. Supported keys: fill_plus, fill_minus, fill_unstranded, col, lwd, row_gap, tip_mm, tip_min_body_mm, link_col, link_lwd, link_lty.

Value

A SeqReadsR6 instance.