## ----warning=F, message=F----------------------------------------------------- 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) 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) 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) 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) 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) 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 ## ---- fig.width=12, fig.height=16--------------------------------------------- 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 ## ----eval=FALSE--------------------------------------------------------------- # ggsave(plot=fwer_sim_fig, file="fwer_simulations.pdf", width=12, height=16)