XGR_plot: Plot annotation peaks: XGR

In RajLabMSSM/echoplot: echoverse module: Locus plot creation for fine-mapping and colocalization studies

Plot annotation peaks: XGR

Description

Import annotation from XGR, filter to only those within the range of dat, and then plot the peaks. If the annotation has already been downloaded previously, it will be reused.

Usage

XGR_plot(
  dat,
  lib_name = "ENCODE_TFBS_ClusteredV3_CellTypes",
  locus_dir = tempdir(),
  palette = get_palettes(n_pals = 1, names_only = TRUE),
  fill_var = "Assay",
  facet_var = "Source",
  geom = "density",
  n_top = 5,
  adjust = 0.2,
  force_new = FALSE,
  show_plot = FALSE,
  nThread = 1,
  verbose = TRUE
)

Arguments

dat	data.table with at least the following columns: SNP SNP RSID CHR chromosome POS position
lib_name	Which XGR annotations to check overlap with. For full list of libraries see here. Passed to the RData.customised argument in xRDataLoader.
locus_dir	Locus-specific directory.
palette	Any palette available in pals. See get_palettes for a list of all palettes.
fill_var	Fill variable.
facet_var	Row facet variable.
geom	Plot type ("density", or "histogram").
n_top	Number of top annotations to be plotted (passed to XGR_filter_sources and then XGR_filter_assays).
adjust	The granularity of the peaks.
force_new	Download and prepare a new query even if the file already exists locally (Default: FALSE).
show_plot	Print the plot.
nThread	Number of threads to parallelise downloading annotations over.
verbose	Print messages.

Value

List with the "data" and the "plot".

Examples

xgr_out <- echoplot::XGR_plot(dat = echodata::BST1[seq_len(1000),])

RajLabMSSM/echoplot documentation built on Oct. 24, 2023, 2:41 a.m.