pleio_plot {pleiotest}

Pleiotropic manhattan plot

Description

Plots the p-values that test the hypothesis of pleiotropic effects on n_traits. This function also returns a dataframe with information of the significant SNPs.

Usage

pleio_plot(
  pleio_res,
  alpha = "bonferroni05",
  n_traits = 2,
  bp_positions = NULL,
  set_colors = NULL,
  set_text = NULL,
  set_plot = TRUE,
  chr_spacing = 1e+05,
  ...
)

Arguments

pleio_res

object returned by pleio_test().

alpha

numeric threshold for significance level (Bonferroni correction by default).

n_traits

integer indicating the level of pleiotropy to test (a.k.a. number of traits).

bp_positions

dataframe with colnames 'chr' and 'pos' indicating the chromosome and position for each SNP. Rownames must contain SNP names matching results of pleio_test.

set_colors

string with 3 colors to use in the plot (by default: c('goldenrod4', 'brown4', 'royalblue2')).

set_text

dataframe or matrix with strings to add as text to identify SNPs or genes. Rownames must be SNP names matching results of pleio_test. The first column of the dataframe must have strings to plot as text.

set_plot

logical indicating whether to return the manhattan plot (TRUE by default).

chr_spacing

integer indicating the spacing (in base pair positions) between chromosomes. 1e5 by default.

...

additional graphic parameters for the plot.

Value

Manhattan plot and dataframe with information related to significant SNPs.