plot_mht: 'manhattan plot'

In yangjl/huskeR: Genomic and Genetic analysis Pipeline on HPC

Description

manhattan plot

Usage

plot_mht(inputdf, hdf = NULL, col2plot = "ModelFreq", jmph = FALSE,
  pl = FALSE, cl_file = "~/bin/zmSNPtools/Rcodes/chr_length_B73v3.csv",
  cex = 0.9, pch = 16, col = rep(c("slateblue", "cyan4"), 5),
  GAP = 5e+06, yaxis = NULL, ...)

newpos(d, GAP, cl)

chrline_tick(GAP, cl)

Arguments

inputdf	An input data.frame to plot. If a cex weight column "cw" presents, dots will be bigger for larger value. plot_mht: [df, =col2plot, "chr", "pos", "cw"(optional)]
hdf	A data.frame contains regions to be highlighted in the manhanttan plot. [df, =NULL, required columns: "chr", "pos"]
col2plot	The column name to plot. [chr, ="ModelFreq"]
jmph	Plot joint mht. [logical, =FALSE], if =TURE, must have cex weight column (cw) in inputdf: [,cw].
pl	Plot lines instead of dots. [logical, =FALSE]
cl_file	The full path of the chromosome length file. [chr, ="~/bin/zmSNPtools/Rcodes/chr_length_B73v3.csv"]
GAP	The physical gap value between chrs. [num, =5e+06]
...	Pass parameters to plot.

yangjl/huskeR documentation built on Sept. 2, 2021, 5:38 a.m.