MOTIFBREAKR_plot: Plot 'motifbreakR' results

In RajLabMSSM/echoannot: echoverse module: Annotate fine-mapping results

Plot motifbreakR results

Description

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
)

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.

Details

Notes:

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

Value

Named list of motif plot paths.

Source

Publication GitHub Viewport bug

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)  
## Not run: 
plot_paths <- MOTIFBREAKR_plot(mb_res = mb_res) 

## End(Not run)

RajLabMSSM/echoannot documentation built on Oct. 26, 2023, 2:41 p.m.