Manhattan plot with genes using plotgardener

data_and_gene.R

library(plotgardener)
par <- pgParams(
  chrom = "chr1", 
  chromstart = 8.2e6,
  chromend = 8.7e6,
  assembly = "hg19",
  just = c("left", "bottom")
)
dat <- data.frame(chrom="chr1", pos=840:849 * 1e4 + 1, p=1:10/10)
pageCreate(width = 4, height = 3.5, showGuides = TRUE)

mp <- plotManhattan(dat, params = par, x = .5, y = 1, width = 3, height = .75, range=c(0, 1.1))
annoGenomeLabel(plot = mp, x = 0.5, y = 1.01)
annoYaxis(plot = mp, at = c(0, .5, 1), axisLine = TRUE, fontsize=8)
plotText(label = "XYZ", x = 0.15, y = .65, rot = 90, fontsize=8)

mp2 <- plotManhattan(dat, params = par, x = .5, y = 2, width = 3, height = .75, range=c(0, 1.1))
annoGenomeLabel(plot = mp2, x = 0.5, y = 2.01)
annoYaxis(plot = mp2, at = c(0, .5, 1), axisLine = TRUE, fontsize=8)
plotText(label = "XYZ", x = 0.15, y = 1.65, rot = 90, fontsize=8)

plotGenes(params = par, x = .5, y = 3.5, width = 3, height = 1)