Nothing
suppressPackageStartupMessages({
require(data.table)
require(jsonlite)
require(ggplot2)
require(cowplot)
})
#' @example
#' .args <- c("results/fig-scales.rda", "results/scan-rois.rds", "results/scan-params.rds", "results/fig-scan.png")
.args <- commandArgs(trailingOnly = T)
load(.args[1])
refpars <- readRDS(.args[3])[, seropos := 1 - seroneg9 ]
reducedrois <- readRDS(.args[2])[mechanism == "binary"][
refpars, on = .(foi, disparity)
][, .(roi = max(roi)),
by = .(foi, disparity, seropos, p_H, log10OR, nu, tau)
]
rename <- function(res, ref) { names(res) <- ref; return(res) }
foiref <- refpars[, seropos[1], by = .(ref = foi)][, rename(V1, ref)]
pHref <- refpars[, p_H[1], by = .(ref = disparity)][, rename(V1, ref)]
ORref <- refpars[, log10OR[1], by = .(ref = disparity)][, rename(V1, ref)]
disref <- list(
md = quote(Disparity ~ (p[H] * ", " * log[10] * OR)),
ll = quote(phantom("Disparity" ~ (p[H] * ", " * log[10] * OR))),
ul = quote(phantom("Disparity" ~ (p[H] * ", " * log[10] * OR)))
)
p <- ggplot(reducedrois) + aes(
log10(tau), nu,
fill = roi, z = roi, color = c("neg", "pos")[(roi > 0) + 1]
) +
facet_grid(
disparity ~ foi,
labeller = label_bquote(
cols = .(
sprintf("%s\n%d%%",
ifelse(foi == "md", "% Seropositive 9-year-olds", ""),
foiref[foi] * 100)
),
rows = atop(
.(
disref[[disparity]]),
(.(pHref[disparity]) * ", " * .(ORref[disparity]))
)
), scales = "free"
) +
geom_heat +
thm + scale_contour + scale_roi + scale_nu + scale_tau
save_plot(tail(.args, 1), p, ncol = 3, nrow = 3, base_height = 4 * 2 / 3)
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