Plot annotation peaks: XGR — XGR

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.

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),])
#> echoannot:: Plotting XGR annotations.
#> Start at 2022-12-23 02:21:55.261217
#> 
#> 'ENCODE_TFBS_ClusteredV3_CellTypes' (from http://galahad.well.ox.ac.uk/bigdata/ENCODE_TFBS_ClusteredV3_CellTypes.RData) has been loaded into the working environment (at 2022-12-23 02:22:02.846536)
#> 
#> End at 2022-12-23 02:22:02.84689
#> Runtime in total is: 7 secs
#> Converting dat to GRanges object.
#> 398 query SNP(s) detected with reference overlap.
#> Warning: Ignoring unknown parameters: `facets`
#> Warning: no non-missing arguments to max; returning -Inf