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.
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,
...
)object returned by pleio_test().
numeric threshold for significance level (Bonferroni correction by default).
integer indicating the level of pleiotropy to test (a.k.a. number of traits).
dataframe with colnames 'chr' and 'pos' indicating the chromosome and position for each SNP. Rownames must contain SNP names matching results of pleio_test.
string with 3 colors to use in the plot (by default: c('goldenrod4', 'brown4', 'royalblue2')).
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.
logical indicating whether to return the manhattan plot (TRUE by default).
integer indicating the spacing (in base pair positions) between chromosomes. 1e5 by default.
additional graphic parameters for the plot.
Manhattan plot and dataframe with information related to significant SNPs.