mxr_manhattan: Generate the manhattan plot.
In roslen/mxr: A Package of GWAS Pipeline Building Blocks

Description Usage Arguments Details

mxr_manhattan generates the manhattan plot of the GWAS results.

mxr_manhattan(gwas_results = "", chr = "CHR", bp = "BP", p = "P",
  snp = "SNP", suggestive_line = -log10(1e-05),
  genomewide_line = -log10(1e-07), highlight = NULL, xlim = 10,
  ylim = 20, file_prefix = "", width = 5, height = 5, unit = "in",
  res = 300, mar = c(5, 4, 4, 0) + 0.1, mgp = c(3, 0.8, 0),
  cex.axis = 0.8, main = "", y_tickmarks = "", y_tickmark_labels = "",
  manhattan = T, qq = T)

`gwas_results`	The fullpath to the GWAS results. The file must have a header line indicating the snp_id, chromosome, pvalue, and base-pair position.
`chr`	Header name of chromosome column.
`bp`	Header for base-pair position.
`p`	Header for the p-value column.
`snp`	Header for the SNP ID column.
`suggestive_line`	Default -log10(1e-5). Set to FALSE to disable.
`highlight`	Character vector of SNPs to highlight in the manhattan plot.
`xlim`	Maximum x-axis value (for the qq plot).
`ylim`	Maximum y-axis value.
`file_prefix`	Fullpath and prefix for manhattan and qq plot file names.
`width`	Width (in inches) of the figure.
`height`	Height (in inches) of the figure.
`unit`	Default: "in" (inches).
`res`	Resolution of the image.
`mar`	Vector of margins.
`mgp`	The mgp vector in plot.
`manhattan`	Set to TRUE to generate Manhattan plot.
`qq`	Set to TRUE to generate QQ plot.
`genomewideline`	Default -log10(1e-7). Set to FALSE to disable.