## ----warning=FALSE, message=FALSE------------------------------------------ library("ggplot2") library("cowplot") ## -------------------------------------------------------------------------- set.seed(1) m <- 10000 binwidth <- 0.025 # generic function to add some properties to gg histograms gg_hist_aesthetic <- function(gg_obj, ylim_max=650) { gg_obj + scale_x_continuous(expand = c(0.02, 0)) + scale_y_continuous(expand = c(0.02, 0), limits=c(0,ylim_max)) + xlab("p-value")+ ylab("Counts")+ theme(axis.title = element_text(face="bold",size=rel(0.1)) ) } ## -------------------------------------------------------------------------- pv_unif <- data.frame(pvalue=runif(m)) gg_unif <- ggplot(pv_unif, aes(x=pvalue)) + geom_histogram(binwidth = binwidth, boundary = 0, colour="lightgrey", fill="#939598") + geom_hline(yintercept=m*binwidth, size=2, col="darkblue") gg_unif <- gg_hist_aesthetic(gg_unif) gg_unif ## ----eval=FALSE------------------------------------------------------------ # ggsave(plot=gg_unif, file="stratified_histograms_unif.pdf", width=4, height=3) ## -------------------------------------------------------------------------- pv_beta_1 <- data.frame(pvalue=c(runif(9000), rbeta(1000,0.5,7))) gg_beta_1 <- ggplot(pv_beta_1, aes(x=pvalue)) + geom_histogram(binwidth = binwidth, boundary = 0, colour="lightgrey", fill="#939598") + geom_hline(yintercept=9000*binwidth, size=1.3, col="darkblue") gg_beta_1 <- gg_hist_aesthetic(gg_beta_1) gg_beta_1 ## ----eval=FALSE------------------------------------------------------------ # ggsave(plot=gg_beta_1, file="stratified_histograms_beta1.pdf", width=4, height=3) ## -------------------------------------------------------------------------- pv_beta_2 <- data.frame(pvalue=c(runif(5500), rbeta(4500,1,4))) gg_beta_2 <- ggplot(pv_beta_2, aes(x=pvalue)) + geom_histogram(binwidth = binwidth, boundary = 0, colour="lightgrey", fill="#939598") + geom_hline(yintercept=5500*binwidth, size=1.3, col="darkblue") gg_beta_2 <- gg_hist_aesthetic(gg_beta_2) gg_beta_2 ## ----eval=FALSE------------------------------------------------------------ # ggsave(plot=gg_beta_2, file="stratified_histograms_beta2.pdf", width=4, height=3) ## ----fig.width=12, fig.height=4-------------------------------------------- gg_stratified <- plot_grid(gg_unif, gg_beta_1, gg_beta_2, nrow=1, labels=c("a)", "b)", "c)")) gg_stratified ## ----eval=FALSE------------------------------------------------------------ # ggsave(plot=gg_stratified, file="stratified_histograms.pdf", width=12, height=4) ## -------------------------------------------------------------------------- set.seed(1) m <- 10000 binwidth <- 0.05 grey <- "grey41" # generic function to add some properties to gg histograms gg_hist_aesthetic <- function(gg_obj, ylim_max=6) { gg_obj + aes(y=..density..)+ scale_x_continuous(expand = c(0.02, 0), breaks=c(0,0.5,1)) + scale_y_continuous(expand = c(0.02, 0), limits=c(0,ylim_max)) + xlab("p-value")+ ylab("Density")+ theme(axis.title = element_text(face="bold",size=rel(0.7))) } ## -------------------------------------------------------------------------- pv_unif <- data.frame(pvalue=runif(m)) gg_unif <- ggplot(pv_unif, aes(x=pvalue)) + geom_histogram(binwidth = binwidth, boundary = 0, colour=grey, fill="lightgrey") gg_unif <- gg_hist_aesthetic(gg_unif) gg_unif ## -------------------------------------------------------------------------- pv_beta_a <- data.frame(pvalue=c(runif(9000), rbeta(1000,0.5,4))) gg_beta_a <- ggplot(pv_beta_a, aes(x=pvalue)) + geom_histogram(binwidth = binwidth, boundary = 0, colour=grey, fill="lightgrey") gg_beta_a <- gg_hist_aesthetic(gg_beta_a) gg_beta_a ## -------------------------------------------------------------------------- pv_beta_b <- data.frame(pvalue=c(runif(8000), rbeta(2000,0.5,11))) gg_beta_b <- ggplot(pv_beta_b, aes(x=pvalue)) + geom_histogram(binwidth = binwidth, boundary = 0, colour=grey, fill="lightgrey") gg_beta_b <- gg_hist_aesthetic(gg_beta_b, ylim_max=5.5) gg_beta_b ## -------------------------------------------------------------------------- pv_all <- rbind(pv_unif, pv_beta_b, pv_beta_a) gg_all <- ggplot(pv_all, aes(x=pvalue)) + geom_histogram(binwidth = binwidth, boundary = 0, colour=grey, fill="lightgrey") gg_all <- gg_hist_aesthetic(gg_all) gg_all ## ----fig.width=6, fig.height=2--------------------------------------------- gg_stratified <- plot_grid(gg_all, gg_beta_b, gg_beta_a, gg_unif, nrow=1, labels=c("a)", "b)", "c)","d)")) gg_stratified ## ----eval=FALSE------------------------------------------------------------ # ggsave(plot=gg_stratified, file="stratified_histograms.pdf", width=6, height=2)