pleio_ideogram {pleiotest}

Plot ideogram from pleio_test results

Description

Plots genomic segments that contain significant pleiotropic SNPs using results of pleio_test(). It also returns a dataframe with segment information.

Usage

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,
  ...
)

Arguments

pleio_res

list 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.

window_size

numeric value indicating the minimum size (in base pairs) of the genomic region that contains significant SNPs.

centromeres

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.

color_bias

number for bias of the color scale. See help(colorRampPalette). By default color_bias = 1

set_plot

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

set_legend

logical indicating whether to plot a legend (TRUE by default).

set_ylim_prop

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.

Value

Ideogram plot and a dataframe with genomic segments information.

See Also

pleio_plot