Plot motifbreakR results — MOTIFBREAKR

Plot motif disruption results generated by MOTIFBREAKR.

Usage

MOTIFBREAKR_plot(
  mb_res,
  mb_filter = NULL,
  rsid = NULL,
  effect = c("strong", "weak"),
  results_dir = file.path(tempdir(), "results"),
  height = 3,
  width = 7,
  verbose = TRUE
)

Source

Publication GitHub Viewport bug

Arguments

mb_res: Results generated by MOTIFBREAKR, in GRanges format.
mb_filter: GRanges object used to filter mb_res before plotting.
rsid: Character vector of RSIDs to plot. If NULL, all RSIDs in mb_res are used.
effect: Character vector of effect strengths to include (e.g. "strong", "weak").
results_dir: Directory where results should be saved as a file named: <results_dir>/_genome_wide/motifbreakR/motifbreakR_results.rds. If NULL, results will not be saved to disk.
height: the height of the device.
width: the width of the device.
verbose: Print messages.

Value

Named list of motif plot paths.

Details

Notes:

Saving as a PDF seems to work much better than PNG format (at least when using grDevices).

Examples

if (FALSE) { # \dontrun{
library(BSgenome) ## <-- IMPORTANT!
library(BSgenome.Hsapiens.UCSC.hg19) ## <-- IMPORTANT!
#### Example fine-mapping results ####
merged_DT <- echodata::get_Nalls2019_merged()
#### Run motif analyses ####
mb_res <- MOTIFBREAKR(rsid_list = c("rs11175620"),
                      # limit the number of datasets tested
                      # for demonstration purposes only
                      pwmList_max = 5,
                      calculate_pvals = FALSE)
plot_paths <- MOTIFBREAKR_plot(mb_res = mb_res)
} # }