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Panel 1: dense arm against sparse arm, every system

Source: R/report.R
dmsa_plot_systems.Rd

Distance from the diagonal is how concentrated a system's response is: a system null on the pooled arm and strong on the max-gene arm carries its signal in one gene.

Usage

dmsa_plot_systems(
  systems,
  alpha = 0.05,
  file = NULL,
  width = 1500,
  height = 1400,
  res = 190
)

Arguments

systems

data.frame with columns system, outcome, p_dense, p_sparse; optionally primary (logical) and top_gene.

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

Invisibly, the plotted data frame.

Examples

## Distance from the diagonal says how concentrated a system's response is:
## strong on the sparse arm only means the signal sits in a single gene.
sys <- data.frame(
  system   = c("HPA axis", "Oxytocin", "Serotonin", "Inflammation"),
  outcome  = "PTSD severity",
  p_dense  = c(0.0004, 0.08, 0.41, 0.62),
  p_sparse = c(0.0012, 0.0003, 0.33, 0.55),
  primary  = c(TRUE, TRUE, FALSE, FALSE),
  top_gene = c("NR3C1", "OXTR", "TPH2", "IL6"))
dmsa_plot_systems(sys, file = tempfile(fileext = ".png"))