IHWpaper 1.18.0
In this vignette we want to generate plots for the same simulations shown in simulations_vignette.Rmd, but this time for FWER control. In particular, we applied the IHW-Bonferroni methods and Bonferroni methods using exactly the same settings as in the above simulations.
library("ggplot2")
library("grid")
library("dplyr")
library("cowplot")
library("IHWpaper")
library("wesanderson")
colors <- wes_palette("Cavalcanti1")[c(3,5)]
null_folder <- system.file("simulation_benchmarks/result_files/ihw_bonf_null",
package = "IHWpaper")
null_sim <- bind_rows(lapply(file.path(null_folder,list.files(null_folder)), function(x) readRDS(x))) %>%
mutate(fdr_method = ifelse(fdr_method == "IHW-Bonferroni E3", "IHW-Bonferroni", fdr_method))
last_vals_a <- group_by(null_sim, fdr_method) %>% summarize(last_vals = max(FDR)) %>%
mutate(last_vals = last_vals + c(+0.003,-0.003),
label = fdr_method,
colour = colors)
## `summarise()` ungrouping output (override with `.groups` argument)
panel_a <- ggplot(null_sim, aes(x=alpha, y=FDR, col=fdr_method)) +
geom_line(size=1.2) +
geom_abline(linetype="dashed") +
xlab(expression(bold(paste("Nominal ",alpha)))) +
ylab("FWER")+
scale_x_continuous(limits= c(0.01,0.1), breaks=seq(0.01,0.09,length=5)) +
#ylim(0,0.9) +
theme(plot.margin = unit(c(3, 7.5, .2, .2), "lines"))+
scale_color_manual(values=colors)+
theme(axis.title = element_text(face="bold") )
panel_a <- pretty_legend(panel_a, last_vals_a, 0.102)
panel_a
ttest_folder <- system.file("simulation_benchmarks/result_files/ihw_bonf_du_ttest_informative",
package = "IHWpaper")
ttest_sim <- bind_rows(lapply(file.path(ttest_folder,list.files(ttest_folder)), function(x) readRDS(x))) %>%
mutate(fdr_method = ifelse(fdr_method == "IHW-Bonferroni E3", "IHW-Bonferroni", fdr_method))
last_vals_b <- group_by(ttest_sim, fdr_method) %>% summarize(last_vals = FDR[which.max(eff_size)]) %>%
mutate(last_vals = last_vals,
label = fdr_method,
colour = colors)
## `summarise()` ungrouping output (override with `.groups` argument)
panel_b <- ggplot(ttest_sim, aes(x=eff_size, y=FDR, col=fdr_method)) +
geom_hline(yintercept=0.1, linetype="dashed") +
geom_line(size=1.2) +
xlab("Effect size") +
ylab("FWER")+
theme(plot.margin = unit(c(3, 7.5, .2, .2), "lines"))+
scale_color_manual(values=colors) +
theme(axis.title = element_text(face="bold") )
panel_b <- pretty_legend(panel_b, last_vals_b, 2.52 )
panel_b
last_vals_c <- group_by(ttest_sim, fdr_method) %>% summarize(last_vals = power[which.max(eff_size)]) %>%
mutate(last_vals = last_vals,
label = fdr_method,
colour = colors)
## `summarise()` ungrouping output (override with `.groups` argument)
panel_c <- ggplot(ttest_sim, aes(x=eff_size, y=power, col=fdr_method)) +
geom_line(size=1.2) +
xlab("Effect size") +
ylab("Power")+
theme(plot.margin = unit(c(3, 7.5, .2, .2), "lines"))+
scale_color_manual(values=colors)+
theme(axis.title = element_text(face="bold") )
panel_c <- pretty_legend(panel_c, last_vals_c, 2.52 )
panel_c
size_investing_folder <- system.file("simulation_benchmarks/result_files/ihw_bonf_wasserman_normal",
package = "IHWpaper")
size_investing_sim <- bind_rows(lapply(file.path(size_investing_folder,
list.files(size_investing_folder)), function(x) readRDS(x))) %>%
mutate(fdr_method = ifelse(fdr_method == "IHW-Bonferroni E3", "IHW-Bonferroni", fdr_method))
last_vals_d <- group_by(size_investing_sim, fdr_method) %>% summarize(last_vals = log10(FDR[which.max(xi_max)])) %>%
mutate(last_vals = last_vals + c(+2.5,-0.8)*0.08,
label = fdr_method,
colour = colors)
## `summarise()` ungrouping output (override with `.groups` argument)
panel_d <- ggplot(size_investing_sim, aes(x=xi_max, y=log10(FDR), col=fdr_method)) +
geom_line(size=1.2) +
xlab(expression(bold(xi[max])))+
ylab("log10(FWER)")+
geom_hline(yintercept=-1, linetype="dashed") +
theme(plot.margin = unit(c(3, 7.5, .2, .2), "lines"))+
scale_color_manual(values=colors) +
theme(axis.title = element_text(face="bold") )
panel_d <- pretty_legend(panel_d, last_vals_d, 6.02 )
panel_d
last_vals_e <- group_by(size_investing_sim, fdr_method) %>% summarize(last_vals = power[which.max(xi_max)]) %>%
mutate(last_vals = last_vals + c(-0.01,+0.01) ,
label = fdr_method,
colour = colors)
## `summarise()` ungrouping output (override with `.groups` argument)
panel_e <- ggplot(size_investing_sim, aes(x=xi_max, y=power, col=fdr_method)) +
geom_line(size=1.2) +
ylab("Power") +
xlab(expression(bold(xi[max])))+
theme(plot.margin = unit(c(3, 7.5, .2, .2), "lines"))+
scale_color_manual(values=colors) +
theme(axis.title = element_text(face="bold") )
panel_e <- pretty_legend(panel_e, last_vals_e, 6.02 )
panel_e
fwer_sim_fig <- plot_grid(panel_a, ggdraw(),
panel_b, panel_c,
panel_d, panel_e,
nrow=3,
labels=c("a)", "", "b)", "c)","d)", "e)"))
fwer_sim_fig