Nothing
# Function for dput'ting objects into a character string
cput <- function(x) {
f <- tempfile()
dput(x, file = f)
return(readLines(f))
}
# Function for plotting meta results
meta_plot <- function(fit, # A fitted object data
idr, # Output from get.IDR
plot_type = c("rank", "gmm", "obs"),
col_sel,
row_sel,
col = c(rep = "steelblue", irrep = "#00000050", sel = "red"),
pch = c(rep = 1, irrep = 1, sel = 16)) {
if (is.null(col_sel) || length(col_sel) < 2) {
i <- 1
j <- 2
} else {
i <- match(col_sel[1], colnames(fit$u))
j <- match(col_sel[2], colnames(fit$u))
}
# Get ranked data
if (plot_type == "rank") {
x <- fit$u
} else if (plot_type == "gmm") {
x <- GMCM:::qgmm.marginal(fit$u, theta = meta2full(fit[[1]], d = ncol(fit$u)))
} else if (plot_type == "obs") {
x <- fit$x
} else {
stop("plot_type not found")
}
# Colour selected rows and reproducible
n <- nrow(x)
cols <- rep(col["irrep"], n)
pchs <- rep(pch["irrep"], n)
# Color by classification
repro <- idr$Khat == 2
cols[repro] <- col["rep"]
pchs[repro] <- pch["rep"]
cols[row_sel] <- col["sel"]
pchs[row_sel] <- pch["sel"]
rows_selected <- (seq_len(n) %in% row_sel)
o <- order(repro, rows_selected)
# Do plot
plot(x = x[o, i],
y = x[o, j],
xlab = colnames(fit$u)[i],
ylab = colnames(fit$u)[j],
axes = FALSE,
main = "",
col = cols[o],
pch = pchs[o],
asp = 1)
axis(1)
axis(2)
}
# Function for plotting meta results
full_plot <- function(fit, # A fitted object data
comp, # Output from get.IDR
plot_type = c("rank", "gmm", "obs"),
col_sel,
row_sel,
pch = 16) {
if (is.null(col_sel) || length(col_sel) < 2) {
i <- 1
j <- 2
} else {
i <- match(col_sel[1], colnames(fit$u))
j <- match(col_sel[2], colnames(fit$u))
}
# Get ranked data
if (plot_type == "rank") {
x <- fit$u
} else if (plot_type == "gmm") {
x <- GMCM:::qgmm.marginal(fit$u, theta = fit$theta)
} else if (plot_type == "obs") {
x <- fit$x
} else {
stop("plot_type not found")
}
# Color by classification
n <- nrow(x)
m <- max(comp)
cols <- rainbow(m)[comp]
cols[is.na(comp)] <- "grey"
# Set color and type for selected rows
cols[row_sel] <- "black"
pchs <- rep(pch, n)
pchs[row_sel] <- 4
# Get order to draw selected rows last
rows_selected <- (seq_len(n) %in% row_sel)
o <- order(rows_selected)
# Do plot
plot(x = x[o, i],
y = x[o, j],
xlab = colnames(fit$u)[i],
ylab = colnames(fit$u)[j],
axes = FALSE,
main = "",
col = cols[o],
pch = pchs[o],
asp = 1)
axis(1)
axis(2)
}
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