ADDO_AddDom4_IntePlot: Visulization of An Integrated Figure (STEP4 of The Add-Dom...

In LeileiCui/ADDO: a comprehensive toolkit to detect, classify and visualise additive and non-additive Quantitative Trait Loci

Description

Visualizing additive and non-additive QTLs by an integrated plot.

Usage

ADDO_AddDom4_IntePlot(outdir = outdir, PheList_Choose = F,
  PheList = PheList, covariates_sum = covariates_sum,
  RegionMan_chr_whole = F, RegionMan_chr_region = RegionMan_chr_region,
  Down_sampling = F, Down_sampling_logP = 1,
  Down_sampling_distance = 10, Plot_model = "NvsAD",
  chrs_sum = chrs_sum, num_nodes = 10)

Arguments

outdir	A character. The output directory where generates the folder: "3_Plot".
PheList_Choose	A logic variable. T: Just investigate specified phenotypes; F: Investigate all phenofiles.
PheList	A vector of character. When choose "PheList_Choose=F", the specified phenotype list must be specified.
covariates_sum	A numeric variable. The sum of all covariates.
RegionMan_chr_whole	A logic variable. T: Draw a whole chromosome; F: Draw the specified region.
RegionMan_chr_region	A numeric variable. The length of specified region around the Peak SNP.
Down_sampling	A logic variable. T: Down-sampling points with low logP to speed up the plotting progress; F: Darwing with all loci.
Down_sampling_logP	A numeric variable. The threshold for down-sampling points for rapid rendering of the Manhattan Plots, when Down_sampling is true.
Down_sampling_distance	A numeric variable. The distance of points for equidistant sampling, when Down_sampling is true.
Plot_model	A character. The model to be mainly focused in the integrated plot. Please select from choose "AvsAD" or "NvsAD" or "NvsA" or "NvsD".
chrs_sum	A numeric variable. The sum of all chromosomes.
num_nodes	A numeric variable. The number of cores used parallelly.

Value

a folder named "3_Plot" with various plots.

Author(s)

Leilei Cui and Bin Yang

Examples

ADDO_AddDom4_IntePlot(outdir=outdir, covariates_sum=2, RegionMan_chr_whole=F, RegionMan_chr_region = 2000000)

LeileiCui/ADDO documentation built on July 25, 2020, 1:51 a.m.