NOTT2019_plac_seq_plot: Plot brain cell-specific interactome data

In RajLabMSSM/echoannot: echoverse module: Annotate fine-mapping results

Plot brain cell-specific interactome data

Description

Plot brain cell-specific interactome data from Nott et al. (2019).

Usage

NOTT2019_plac_seq_plot(
  dat = NULL,
  locus_dir = NULL,
  title = NULL,
  show_plot = TRUE,
  save_plot = TRUE,
  return_interaction_track = FALSE,
  x_limits = NULL,
  zoom_window = NULL,
  index_SNP = NULL,
  genomic_units = "POS",
  color_dict = c(enhancers = "springgreen2", promoters = "purple", anchors = "black"),
  highlight_plac = TRUE,
  show_regulatory_rects = TRUE,
  show_anchors = TRUE,
  strip.text.y.angle = 0,
  xtext = TRUE,
  save_annot = FALSE,
  point_size = 2,
  height = 7,
  width = 7,
  dpi = 300,
  return_as = "Tracks",
  nThread = 1,
  verbose = TRUE
)

Arguments

dat	Fine-mapping results data from finemap_loci.
locus_dir	Locus-specific directory.
title	all title elements: plot, axes, legends (element_text(); inherits from text)
show_plot	Print plot.
save_plot	Whether to save the plot.
return_interaction_track	Return only the interaction track (before completing the plot and showing it).
x_limits	x-axis limits to be applied to all plots (useful when trying to keep a common coordinate system).
zoom_window	Zoom window.
index_SNP	Index/lead SNP RSID.
genomic_units	Which genomic units to return window limits in.
color_dict	Named list of colors for each regulatory element.
highlight_plac	Whether to scale opacity of PLAC-seq interactions (arches) such that interactions with anchors containing Consensus SNPs will be colored darker (Default: TRUE). If FALSE, will instead apply the same opacity level to all interactions.
show_regulatory_rects	Show enhancers/promoters as rectangles.
show_anchors	Show PLAC-seq anchors.
strip.text.y.angle	Angle of the y-axis facet labels.
xtext	Whether to include x-axis title and text.
save_annot	Save the queried subset of bigwig annotations.
point_size	Point size of each SNP in the GWAS/fine-mapping plots.
height	height (defaults to the height of current plotting window)
width	width (defaults to the width of current plotting window)
dpi	dpi to use for raster graphics
return_as	Plot class to convert plot_list to: "ggplot"ggplot "ggbio"ggbio "patchwork"patchwork "Tracks"tracks NULLReturn original object.
nThread	Number of threads to parallelise downloads across.
verbose	Print messages.

Source

Nott et al. (2019)

See Also

Other NOTT2019: NOTT2019_bigwig_metadata, NOTT2019_epigenomic_histograms(), NOTT2019_get_epigenomic_peaks(), NOTT2019_get_interactions(), NOTT2019_get_interactome(), NOTT2019_get_promoter_celltypes(), NOTT2019_get_promoter_interactome_data(), NOTT2019_get_regulatory_regions(), NOTT2019_superenhancers(), get_NOTT2019_interactome(), get_NOTT2019_superenhancer_interactome()

Examples

trks_plus_lines <- echoannot::NOTT2019_plac_seq_plot(dat = echodata::BST1) 

RajLabMSSM/echoannot documentation built on Oct. 26, 2023, 2:41 p.m.