Nothing
plot.TC <-
function (x, iRatios = TRUE, FDR = TRUE, AC = TRUE, WARNINGS = FALSE,
...)
{
ACT <- sum(apply(as.matrix(1:length(x$act)), 1,
function(tp) class(x$act[[tp]]) == "STP")) == length(x$act)
GCT <- sum(apply(as.matrix(1:length(x$gct)), 1,
function(tp) class(x$gct[[tp]]) == "STP")) == length(x$gct)
cols <- FDR + AC
rows <- length(x[[1]])
tPoints <- x$tPoints
if (iRatios) {
par(mfrow = c(1, 1), mar = c(4.5, 4.5, 2.5, 1), las = 1)
barplot(height = 100 * x$iRatios, col = "grey50",
main = "Inertia ratios (%)")
}
if (ACT) {
if (FDR) {
par(oma = c(0, 0, 2, 0))
plot(x$act[[x$activeTP]], FDR, AC = FALSE, WARNINGS,
tp = tPoints[[x$activeTP]])
mtext(paste("Active vs Complementary time points -",
tPoints[x$activeTP]), outer = TRUE, cex = 1.5,
font = 2)
}
if (AC) {
par(mfrow = c(ceiling(rows/2), 2), mar = c(4.5, 4.5,
2.5, 1), oma = c(0, 0, 2, 0), las = 1)
for (tp in 1:length(tPoints)) {
plot(x$act[[tp]], FDR = FALSE, tp = tPoints[tp])
}
mtext(paste("Active vs Complementary time points -",
tPoints[x$activeTP]), outer = TRUE, cex = 1.5,
font = 2)
}
}
if (GCT) {
mf <- if (AC && FDR)
c(1, cols)
else c(ceiling(rows/2), 2)
par(mfrow = mf, mar = c(4.5, 4.5, 2.5, 1), oma = c(0,
0, 2, 0), las = 1)
for (tp in 1:length(tPoints)) {
auxSTP <- x$gct[[tp]]
if (auxSTP$astar > auxSTP$alpha) {
auxSTP$dgenes <- rep("no-diff.", length(auxSTP$dgenes))
auxSTP$tstar <- NA
}
plot(auxSTP, FDR, AC, WARNINGS, tPoints[tp])
if (AC && FDR)
mtext(paste("Group conformation through time -",
tPoints[tp]), outer = TRUE, cex = 1.5, font = 2)
}
if (!(AC && FDR))
mtext("Group conformation through time", outer = TRUE,
cex = 1.5, font = 2)
}
}
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