makeManhattanPlot: Make a Manahattan plot of p-values

In kauralasoo/wiggleplotr: Make read coverage plots from BigWig files

Make a Manahattan plot of p-values

Description

The Manhattan plots is compatible with wiggpleplotr read coverage and transcript strucutre plots. Can be appended to those using the cowplot::plot_grid() function.

Usage

makeManhattanPlot(
  pvalues_df,
  region_coords,
  color_R2 = FALSE,
  data_track = TRUE
)

Arguments

pvalues_df	Data frame of association p-values (required columns: track_id, p_nominal, pos)
region_coords	Start and end coordinates of the region to plot.
color_R2	Color the points according to R2 from the lead variant. Require R2 column in the pvalues_df data frame.
data_track	If TRUE, then remove all information from x-axis. Makes it easy to append to read coverage or transcript strcture plots using cowplot::plot_grid().

Value

gglot2 object

Examples

data = dplyr::data_frame(track_id = "GWAS", pos = sample(c(1:1000), 200), p_nominal = runif(200, min = 0.0000001, 1))
makeManhattanPlot(data, c(1,1000), data_track = FALSE)

kauralasoo/wiggleplotr documentation built on July 4, 2022, 11:43 a.m.