NOTT2019_epigenomic_histograms: Plot brain cell-specific epigenomic data

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

Plot brain cell-specific epigenomic data

Description

Brain cell-specific epigenomic data from Nott et al. (2019).

Usage

NOTT2019_epigenomic_histograms(
  dat,
  bigwig_metadata = echoannot::NOTT2019_bigwig_metadata,
  locus_dir = tempdir(),
  show_plot = TRUE,
  save_plot = FALSE,
  full_data = TRUE,
  return_assay_track = FALSE,
  binwidth = 200,
  density_adjust = 0.2,
  zoom = "1x",
  strip.text.y.angle = 90,
  xtext = TRUE,
  geom = "density",
  plot_formula = "Cell_type ~.",
  fill_var = "Assay",
  genomic_units = "Mb",
  as_ggplot = TRUE,
  dpi = 300,
  height = 15,
  width = 8,
  nThread = 1,
  save_annot = FALSE,
  verbose = TRUE
)

Arguments

dat	Fine-mapping results data from finemap_loci.
bigwig_metadata	Metadata table with at least the following two columns: "name"Unique name of the file. "data_link"URL to UCSC genome browser bigwig file.
locus_dir	Locus-specific directory.
show_plot	Show plot.
save_plot	Whether to save the plot.
full_data	Whether to download the full data (genomic ranges of all sequence reads) as opposed to a reduced representation of the data as a single vector (i.e. the aggregated reads "score"). Setting full_data=TRUE is necessary for creating histograms and density plots.
return_assay_track	Return only the assay track (before adding the rest of the tracks and showing the plot).
binwidth	width of the bins.
density_adjust	Passed to adjust argument in geom_density.
zoom	Zoom into the center of the locus when plotting (without editing the fine-mapping results file). You can provide either: The size of your plot window in terms of basepairs (e.g. zoom=50000 for a 50kb window). How much you want to zoom in (e.g. zoom="1x" for the full locus, zoom="2x" for 2x zoom into the center of the locus, etc.). You can pass a list of window sizes (e.g. c(50000,100000,500000)) to automatically generate multiple views of each locus. This can even be a mix of different style inputs: e.g. c("1x","4.5x",25000).
strip.text.y.angle	Angle of the y-axis facet labels.
xtext	Whether to include x-axis title and text.
geom	Geom to use (Single character for now). Please see section Geometry for details.
plot_formula	Formula passed to facets argument in facet_grid.
fill_var	Variable name to use for plot fill argument.
genomic_units	Which genomic units to return window limits in.
as_ggplot	Return plot as ggplot2 (TRUE) or Tracks (FALSE) object.
dpi	dpi to use for raster graphics
height	height (defaults to the height of current plotting window)
width	width (defaults to the width of current plotting window)
nThread	Number of threads to parallelise downloads across.
save_annot	Save the queried subset of bigwig annotations.
verbose	Print messages.

Source

Nott et al. (2019)

See Also

Other NOTT2019: NOTT2019_bigwig_metadata, NOTT2019_get_epigenomic_peaks(), NOTT2019_get_interactions(), NOTT2019_get_interactome(), NOTT2019_get_promoter_celltypes(), NOTT2019_get_promoter_interactome_data(), NOTT2019_get_regulatory_regions(), NOTT2019_plac_seq_plot(), NOTT2019_superenhancers(), get_NOTT2019_interactome(), get_NOTT2019_superenhancer_interactome()

Examples

nott2019_track <- echoannot::NOTT2019_epigenomic_histograms(
    dat = echodata::BST1, 
    bigwig_metadata = echoannot::NOTT2019_bigwig_metadata[1:2,])

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