Panel 2: gene level inside one system

Usage

dmsa_plot_genes(
  genes,
  null_max = NULL,
  title = "",
  alpha = 0.05,
  file = NULL,
  width = 1500,
  height = 1500,
  res = 190
)

Arguments

genes: data.frame for ONE system and outcome: gene, z, n_probes, optionally p_adj (max-T adjusted) and selected.
null_max: Optional numeric vector of the permutation null of max|z| over the same genes; its .95 and .99 quantiles are drawn as the multiplicity-adjusted thresholds.
title: System label.
alpha: Gate level. The gate is min(1, 2*min(p_dense, p_sparse)), so the boundary drawn is at alpha/2 on each arm.
file: Optional png path. If NULL draws to the current device.
width, height, res: png dimensions.

Value

Called for its side effect of drawing a plot on the active graphics device. Returns NULL invisibly.

Examples

set.seed(1)
genes <- data.frame(gene = paste0("G", 1:8), n_probes = sample(3:9, 8, TRUE),
                    z = c(rnorm(7), 3.6))
genes$p_adj <- 2 * pnorm(-abs(genes$z))
## the permutation null of max|z| over this same family of genes
null_max <- apply(matrix(rnorm(200 * 8), 200, 8), 1, function(r) max(abs(r)))
dmsa_plot_genes(genes, null_max = null_max, title = "HPA axis",
                file = tempfile(fileext = ".png"))