Plots genomic segments that contain significant pleiotropic SNPs using results of pleio_test(). It also returns a dataframe with segment information.
pleio_ideogram(
pleio_res,
alpha = "bonferroni05",
n_traits = 2,
bp_positions,
window_size = 1e+06,
centromeres = NULL,
color_bias = 1,
set_plot = T,
set_legend = T,
set_ylim_prop = 1.1,
...
)list 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.
numeric value indicating the minimum size (in base pairs) of the genomic region that contains significant SNPs.
string 'human' or dataframe (or matrix) with chromosome and position (in mbp) of the centromeres in the first and second columns. If NULL (default) does not plot the centromeres.
number for bias of the color scale. See help(colorRampPalette). By default color_bias = 1
logical indicating whether to plot the ideogram (TRUE by default).
logical indicating whether to plot a legend (TRUE by default).
numeric proportion of upper margin to fit the legend (no margin by default). 1 = no margin, 1.1 = 10% left for margin, etc.
more plot arguments.
Ideogram plot and a dataframe with genomic segments information.