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RAINBOWR (version 0.1.33)

manhattan3: Draw the effects of epistasis (3d plot and 2d plot)

Description

Draw the effects of epistasis (3d plot and 2d plot)

Usage

manhattan3(
  input,
  map,
  cum.pos,
  plot.epi.3d = TRUE,
  plot.epi.2d = TRUE,
  main.epi.3d = NULL,
  main.epi.2d = NULL,
  saveName = NULL
)

Value

Draw 3d plot and 2d plot to show epistatic effects

Arguments

input

List of results of RGWAS.epistasis / RGWAS.twostep.epi. If the output of `RGWAS.epistasis` is `res`, `input` corresponds to `res$scores`. If the output of `RGWAS.twostep.epi.` is `res`, `input` corresponds to `res$epistasis$scores`. See: Value of RGWAS.epistasis

map

Data frame with the marker names in the first column. The second and third columns contain the chromosome and map position. This is map information for SNPs which are tested epistatic effects.

cum.pos

Cumulative position (over chromosomes) of each marker

plot.epi.3d

If TRUE, draw 3d plot

plot.epi.2d

If TRUE, draw 2d plot

main.epi.3d

The title of 3d plot. If this argument is NULL, trait name is set as the title.

main.epi.2d

The title of 2d plot. If this argument is NULL, trait name is set as the title.

saveName

When drawing any plot, you can save plots in png format. In saveName, you should substitute the name you want to save. When saveAt = NULL, the plot is not saved.