Plot IQ Locus — plot_iq_locus • iceqream

This function generates a plot of an IQ locus, including DNA sequence, motif responses, and ATAC-seq tracks.

Usage

plot_iq_locus(
  interval,
  pbm_list,
  atac_tracks,
  width = 500,
  ext_width = 200000,
  T_emax = 8,
  T_rmax = NULL,
  motifs = NULL,
  plot_others = FALSE,
  trim_pbms = TRUE,
  trim_bits_thresh = 0.1,
  bits_threshold = NULL,
  order_motifs = TRUE,
  atac_names = atac_tracks,
  atac_colors = NULL,
  atac_sizes = NULL,
  line_thresh = 0.9,
  title = NULL,
  score = NULL,
  predicted_score = NULL,
  dna = NULL,
  norm_q = 0.995,
  tracks_q = NULL,
  iterator = 20,
  norm_intervals = gintervals.all(),
  atac_smooth = 2,
  ext_atac_smooth = atac_smooth * 5,
  tn5bias_track = "tn5bias",
  normalize_tn5bias = TRUE,
  tss_intervals = "intervs.global.tss",
  exon_intervals = "intervs.global.exon",
  annot_track = NULL,
  annot_track_name = NULL,
  annot_colors = c("#FF9800", "#009688"),
  annot_track_iterator = 1,
  annot_track_smooth = 1,
  annot_intervals = NULL,
  annot_intervals_color = "darkgreen",
  mark_conservation = FALSE,
  conservation_threshold = 1.5,
  scale_cex = 500,
  dna_height = 0.03,
  filename = NULL,
  dev = grDevices::pdf,
  plot_width = 15,
  plot_height = 8,
  base_size = 8,
  base_family = "ArialMT",
  rasterize = FALSE,
  raster_device = "ragg",
  ...
)

Arguments

interval: A genomic interval to plot.
pbm_list: A list of PBM objects.
atac_tracks: A vector of ATAC-seq track names to plot.
width: Width of the plot in bp.
ext_width: Width of the top plot in bp.
T_emax: Numeric, threshold for maximum energy.
T_rmax: Numeric, threshold for maximum response.
motifs: A list of specific motifs to plot.
plot_others: Logical, whether to plot other motifs that pass the threshold when specific motifs are provided.
trim_pbms: Logical, whether to trim PBM objects by removing positions with low information content from the beginning and end of the PSSM.
trim_bits_thresh: Numeric, threshold for trimming PBM objects.
bits_threshold: Numeric, threshold for trimming PSSMs.
order_motifs: Logical, whether to order motifs by maximum response.
atac_names: Character vector, names for ATAC-seq tracks.
atac_colors: Named vector, colors for ATAC-seq tracks.
atac_sizes: Named vector, line sizes for ATAC-seq tracks.
line_thresh: Numeric, threshold for drawing vertical lines.
title: Character, optional title for the plot.
score: Numeric, optional score to display in the plot title.
predicted_score: Numeric, optional predicted score to display in the plot title.
dna: Character, DNA sequence to plot. If NULL, the sequence is extracted from the interval.
norm_q: Numeric, quantile for normalization. If a vector, should have the same length as atac_names.
tracks_q: Data frame, pre-computed quantiles for tracks. Should have a 'type' column and a 'q' column.
iterator: Numeric, iterator for gextract.
norm_intervals: Genomic intervals for normalization.
atac_smooth: Numeric, smoothing factor for ATAC-seq tracks.
ext_atac_smooth: Numeric, smoothing factor for the top plot.
tn5bias_track: Character, name of the Tn5 bias track.
normalize_tn5bias: Logical, whether to normalize using the TN5 bias track. If a vector, should have the same length as atac_names.
tss_intervals: Character, name of the TSS intervals track.
exon_intervals: Character, name of the exon intervals track.
annot_track: Character, name of the annotation track.
annot_track_name: Character, display name for the annotation track.
annot_colors: Named vector, colors for annotation track.
annot_track_iterator: Numeric, iterator for annotation track extraction.
annot_track_smooth: Numeric, smoothing factor for annotation track.
annot_intervals: Genomic intervals for annotation (start positions would be used).
annot_intervals_color: Color for annotation intervals.
mark_conservation: Logical, whether to mark conservation in the DNA sequence.
conservation_threshold: Numeric, threshold for marking conservation.
scale_cex: Numeric, scaling factor for letter sizes.
dna_height: Numeric, height of each row of DNA sequence relative to the entire plot.
filename: Character, output filename (if NULL, plot is not saved).
dev: Function, device to use for plotting.
plot_width: Numeric, width of the output plot.
plot_height: Numeric, height of the output plot.
base_size: Numeric, base font size for the plot.
base_family: Character, base font family for the plot.
rasterize: Logical, whether to rasterize certain plot elements for better performance.
raster_device: Character, device to use for rasterization.
...: additional arguments to pass to the plotting function.

Value

A ggplot object containing the IQ locus plot.