Plot motifbreakR results — MOTIFBREAKR

Plot motif disruption results generated by MOTIFBREAKR.

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; the identifier of the variant to be visualized
effect: Character; show motifs that are strongly effected c("strong"), weakly effected c("weak"), or both c("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

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)  
#> genome_build set to hg19 by default.
#> Using genome_build hg19
#> + MOTIFBREAKR:: Using pre-existing tmp file.
if (FALSE) {
plot_paths <- MOTIFBREAKR_plot(mb_res = mb_res) 
}