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FigureS3.R
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FigureS3.R
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# Note: Run sim-study-sec4-sec5.R, and
# sim-study-sec4-sec5-collate-results.R to
# do the simulation study and format results first
#### Load libraries & functions ####
library(ggplot2)
library(gridExtra)
library(grid)
library(scales)
# Function to arrange plots in a row
grid_arrange_shared_legend <- function(..., nrow = 1, ncol = length(list(...)), position = c("bottom", "right")) {
plots <- list(...)
position <- match.arg(position)
g <- ggplotGrob(plots[[1]] + theme(legend.position = position))$grobs
legend <- g[[which(sapply(g, function(x) x$name) == "guide-box")]]
lheight <- sum(legend$height)
lwidth <- sum(legend$width)
gl <- lapply(plots, function(x) x + theme(legend.position = "none"))
gl <- c(gl, nrow = nrow, ncol = ncol)
combined <- switch(position,
"bottom" = arrangeGrob(do.call(arrangeGrob, gl),
legend,
ncol = 1,
heights = unit.c(unit(1, "npc") - lheight, lheight)),
"right" = arrangeGrob(do.call(arrangeGrob, gl),
legend,
ncol = 2,
widths = unit.c(unit(1, "npc") - lwidth, lwidth)))
grid.draw(combined)
}
#### Generate plots comparing performance of PLRT w/ misspecification, p=10, K=3 ####
p=10
K=3
# Figure S1a
sig=2.4
load(file=paste("df-K", K, "-p", p, "-sig",
sig, ".Rdata", sep=""))
df_comp_per <- df[df$Method %in% c("test_indep_per", "test_indep_perK2",
"test_indep_perK4"), ]
df_comp_per$Method <- factor(df_comp_per$Method,
levels=c("test_indep_per", "test_indep_perK2",
"test_indep_perK4"))
lty <- setNames(c(5, 4, 3, 2, 1), levels(factor(df_comp_per$n)))
p1_comp_per <- ggplot(aes(x = delta, y = power, ymin = power - se, ymax = power + se,
color = df_comp_per$Method,
group = interaction(df_comp_per$n, df_comp_per$Method)),
linetype=lty, data=df_comp_per) +
geom_hline(yintercept=0.05, linetype="dotted") +
annotate(geom="text", label=as.character(expression(alpha==~"0.05")),parse=T,
x=0.08, y=0, vjust=0.3) +
geom_line(aes(linetype=as.factor(df_comp_per$n))) + geom_linerange() +
xlab("Dependence between views") +
ylab("Power at 5% significance level") +
scale_colour_manual(name = "Methods",
labels=c( "Pseudo LRT (K=3, correct K)",
"Pseudo LRT (K=2, K too small)",
"Pseudo LRT (K=4, K too big)"),
values = c("#1b9e77", "#d95f02", "#7570b3")) +
scale_linetype_manual(name = " n ", values=lty) +
ggtitle(expression(sigma==~2.4)) +
theme(plot.title = element_text(hjust = 0.5)) +
theme_gray(base_size = 15.5) + coord_cartesian(ylim = c(0, 1))
p1_comp_per
# Figure S1b
sig=4.8
load(file=paste("df-K", K, "-p", p, "-sig",
sig, ".Rdata", sep=""))
df_comp_per2 <- df[df$Method %in% c("test_indep_per", "test_indep_perK2",
"test_indep_perK4"), ]
df_comp_per2$Method <- factor(df_comp_per2$Method,
levels=c("test_indep_per", "test_indep_perK2",
"test_indep_perK4"))
lty2 <- setNames(c(5, 4, 3, 2, 1), levels(factor(df_comp_per2$n)))
p2_comp_per <- ggplot(aes(x = delta, y = power, ymin = power - se, ymax = power + se,
color = df_comp_per2$Method,
group = interaction(df_comp_per2$n,
df_comp_per2$Method)),
linetype=lty2,
data=df_comp_per2) +
geom_hline(yintercept=0.05, linetype="dotted") +
geom_line(aes(linetype=as.factor(df_comp_per2$n))) + geom_linerange() +
xlab("Dependence between views") +
ylab("") +
scale_colour_manual(name = "Methods",
labels=c( "Pseudo LRT (K=3, correct K)",
"Pseudo LRT (K=2, K too small)",
"Pseudo LRT (K=4, K too big)"),
values = c("#1b9e77", "#d95f02", "#7570b3")) +
scale_linetype_manual(name = " n ", values=lty2) +
ggtitle(expression(sigma==~4.8)) +
theme(plot.title = element_text(hjust = 0.5),
axis.title.y=element_blank(),
axis.ticks.y=element_blank(),
axis.text.y=element_blank()) +
theme_gray(base_size = 15.5) + coord_cartesian(ylim = c(0, 1))
p2_comp_per
# Figure S1c
sig=9.6
load(file=paste("df-K", K, "-p", p, "-sig",
sig, ".Rdata", sep=""))
df_comp_per3 <- df[df$Method %in% c("test_indep_per", "test_indep_perK2",
"test_indep_perK4"), ]
df_comp_per3$Method <- factor(df_comp_per3$Method,
levels=c("test_indep_per", "test_indep_perK2",
"test_indep_perK4"))
lty3 <- setNames(c(5, 4, 3, 2, 1), levels(factor(df_comp_per3$n)))
p3_comp_per <- ggplot(aes(x = delta, y = power, ymin = power - se,
ymax = power + se,
color = df_comp_per3$Method,
group = interaction(df_comp_per3$n,
df_comp_per3$Method)),
linetype=lty3,
data=df_comp_per3) +
geom_hline(yintercept=0.05, linetype="dotted") +
geom_line(aes(linetype=as.factor(df_comp_per3$n))) + geom_linerange() +
xlab("Dependence between views") +
ylab("") +
scale_colour_manual(name = "Methods",
labels=c( "Pseudo LRT (K=3, correct K)",
"Pseudo LRT (K=2, K too small)",
"Pseudo LRT (K=4, K too big)"),
values = c("#1b9e77", "#d95f02", "#7570b3")) +
scale_linetype_manual(name = " n ", values=lty3) +
ggtitle(expression(sigma==~9.6)) +
theme(plot.title = element_text(hjust = 0.5),
axis.title.y=element_blank(),
axis.ticks.y=element_blank(),
axis.text.y=element_blank()) +
theme_gray(base_size = 15.5) + coord_cartesian(ylim = c(0, 1))
p3_comp_per
# Arrange in a row
pdf("FigureS3.pdf", width=12, height=6)
grid_arrange_shared_legend(p1_comp_per, p2_comp_per,
p3_comp_per, nrow=1, ncol=3)
dev.off()