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Plot annotation peaks: XGR

Source: R/XGR_plot.R
XGR_plot.Rd

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 (XGR on CRAN). Passed to the RData.customised argument in XGR::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

if (FALSE) { # \dontrun{
xgr_out <- echoplot::XGR_plot(dat = echodata::BST1[seq_len(1000),])
} # }