Panel 3: probe level, with the CpG-to-expression direction applied

The panel that declares a direction. Each probe's slope is reflected according to its cpgdirection call so that every probe is read on one axis; reflected probes are drawn as open symbols and the convention is printed under the title.

Usage

dmsa_plot_probes(
  probes,
  invert = c("+1", "-1", "none"),
  gene_summary = NULL,
  title = "",
  axis_label = NULL,
  alpha = 0.05,
  file = NULL,
  width = 1700,
  height = 1400,
  res = 190
)

Arguments

probes

data.frame for ONE system and outcome, restricted to the genes worth showing: gene, probe, b, se, d (the cpgdirection call, +1 or -1); optionally p and selected.

invert

Which d is reflected onto the common axis: "+1" (default) reflects the probes whose methylation predicts HIGHER expression, "-1" reflects the others, "none" shows raw slopes.

With "+1" the axis reads: positive = the exposure moves methylation in the direction that LOWERS this gene's expression. Every d = -1 probe is shown as fitted (more methylation, less expression) and every d = +1 probe is reflected so that it means the same thing.

gene_summary

Optional data.frame with gene and z, and optionally p_adj: the pooled gene-level result, drawn as a diamond on its own row. This is usually the point of the figure - individual probes are rarely significant on their own, and the evidence lives in their agreement.

title

System label.

axis_label

Overrides the x-axis 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

## Every probe is read on one axis. A CpG whose methylation predicts HIGHER
## expression (d = +1) is reflected, so positive always means the exposure
## moved methylation the way that LOWERS this gene's expression.
pr <- data.frame(
  gene  = "NR3C1",
  probe = paste0("cg", 10001:10006),
  b     = c(-0.021, -0.014, 0.018, -0.009, 0.026, -0.017),
  se    = c(0.008, 0.007, 0.009, 0.006, 0.010, 0.008),
  d     = c(-1, -1, 1, -1, 1, -1))
dmsa_plot_probes(pr, gene_summary = data.frame(gene = "NR3C1", z = -2.9),
                 title = "HPA axis", file = tempfile(fileext = ".png"))