adcal/vsglint plot improvements

Author: Kieran Elmes

plot_lasso_stats.R

@@ -1,6 +1,7 @@
 #!/usr/bin/Rscript
 library(ggplot2)
 library(dplyr)
+library(Cairo)
 
 gdat = readRDS('PrecRecF1/dat_precrecf1_glinternet') %>%
                 filter(test == "yes") %>%
@@ -20,32 +21,47 @@ ldat_large_adcaltrue  = readRDS('PrecRecF1/dat_precrecf1_lasso') %>%
 ldat_large_limit_nb   = readRDS('PrecRecF1/dat_precrecf1_lasso') %>%
 						filter(n==10000) %>% filter(adcal==FALSE) %>% filter(nbeta_limit == 2000) %>% filter(test=="yes") %>%
 						mutate(time_taken = time_taken + ols_time) %>%
-                 mutate(function_used="Limited beta lasso")
+                 mutate(function_used="Limited-\U03B2 lasso")
 
 vsglint_dat= bind_rows(ldat_large_limit_nb, gdat)
 adcal_dat = bind_rows(ldat_small_adcalfalse, ldat_small_adcaltrue)
 large_adcal_limit_nb_dat = bind_rows(ldat_large_adcaltrue, ldat_large_limit_nb)
 
-vsglint_precision_plot = ggplot(vsglint_dat, aes(x=function_used, y=precision)) + geom_boxplot() + theme_bw()
-vsglint_recall_plot = ggplot(vsglint_dat, aes(x=function_used, y=recall)) + geom_boxplot() + theme_bw()
-vsglint_time_taken_plot = ggplot(vsglint_dat, aes(x=function_used, y=time_taken)) + scale_y_continuous(trans='log10') + geom_boxplot() + theme_bw()
+vsglint_precision_plot = ggplot(vsglint_dat, aes(x=function_used, y=precision)) + geom_boxplot() + theme_bw() + theme(axis.title.x = element_blank()) + labs(y = "Precision")
+vsglint_recall_plot = ggplot(vsglint_dat, aes(x=function_used, y=recall)) + geom_boxplot() + theme_bw() + theme(axis.title.x = element_blank()) + labs(y = "Recall")
 
-ggsave(vsglint_precision_plot, file="plots/vsglint_precision_plot.pdf", width=2.5, height=3)
-ggsave(vsglint_recall_plot, file="plots/vsglint_recall_plot.pdf", width=2.5, height=3)
-ggsave(vsglint_time_taken_plot, file="plots/vsglint_time_plot.pdf", width=2.5, height=3)
 
-adcal_precision_plot = ggplot(adcal_dat, aes(x=function_used, y=precision)) + geom_boxplot() + theme_bw()
-adcal_recall_plot = ggplot(adcal_dat, aes(x=function_used, y=recall)) + geom_boxplot() + theme_bw()
-adcal_time_taken_plot = ggplot(adcal_dat, aes(x=function_used, y=time_taken)) + scale_y_continuous(trans='log10') + geom_boxplot() + theme_bw()
+vsglint_time_taken_plot = ggplot(vsglint_dat, aes(x=function_used, y=time_taken)) + scale_y_continuous(trans='log10') + geom_boxplot() + theme_bw() + theme(axis.title.x = element_blank()) + labs(y = "Time Taken (s)")
 
-ggsave(adcal_precision_plot,  file="plots/small_adcal_precision_plot.pdf", width=3, height=4)
-ggsave(adcal_recall_plot,     file="plots/small_adcal_recall_plot.pdf", width=3, height=4)
-ggsave(adcal_time_taken_plot, file="plots/small_adcal_time_plot.pdf", width=3, height=4)
 
-large_adcal_limit_nb_precision_plot  = ggplot(large_adcal_limit_nb_dat, aes(x=function_used, y=precision)) + geom_boxplot() + theme_bw()
-large_adcal_limit_nb_recall_plot     = ggplot(large_adcal_limit_nb_dat, aes(x=function_used, y=recall)) + geom_boxplot() + theme_bw()
-large_adcal_limit_nb_time_taken_plot = ggplot(large_adcal_limit_nb_dat, aes(x=function_used, y=time_taken)) + scale_y_continuous(trans='log10') + geom_boxplot() + theme_bw()
 
-ggsave(large_adcal_limit_nb_precision_plot,  file="plots/large_adcal_limit_nb_precision_plot.pdf", width=3, height=4)
-ggsave(large_adcal_limit_nb_recall_plot,     file="plots/large_adcal_limit_nb_recall_plot.pdf", width=3, height=4)
-ggsave(large_adcal_limit_nb_time_taken_plot, file="plots/large_adcal_limit_nb_time_plot.pdf", width=3, height=4)
+ggsave(vsglint_precision_plot, file="plots/vsglint_precision_plot.pdf", width=2.6, height=3, device=cairo_pdf)
+ggsave(vsglint_recall_plot, file="plots/vsglint_recall_plot.pdf", width=2.6, height=3, device=cairo_pdf)
+ggsave(vsglint_time_taken_plot, file="plots/vsglint_time_plot.pdf", width=2.6, height=3, device=cairo_pdf)
+
+adcal_precision_plot = ggplot(adcal_dat, aes(x=function_used, y=precision)) + geom_boxplot() + theme_bw() + theme(axis.title.x = element_blank()) + labs(y = "Precision")
+
+
+adcal_recall_plot = ggplot(adcal_dat, aes(x=function_used, y=recall)) + geom_boxplot() + theme_bw() + theme(axis.title.x = element_blank()) + labs(y = "Recall")
+
+
+adcal_time_taken_plot = ggplot(adcal_dat, aes(x=function_used, y=time_taken)) + scale_y_continuous(trans='log10') + geom_boxplot() + theme_bw() + theme(axis.title.x = element_blank()) + labs(y = "Time Taken (s)")
+
+
+ggsave(adcal_precision_plot,  file="plots/small_adcal_precision_plot.pdf", width=2.6, height=3, device=cairo_pdf)
+ggsave(adcal_recall_plot,     file="plots/small_adcal_recall_plot.pdf", width=2.6, height=3, device=cairo_pdf)
+ggsave(adcal_time_taken_plot, file="plots/small_adcal_time_plot.pdf", width=2.6, height=3, device=cairo_pdf)
+
+large_adcal_limit_nb_precision_plot  = ggplot(large_adcal_limit_nb_dat, aes(x=function_used, y=precision)) + geom_boxplot() + theme_bw() + theme(axis.title.x = element_blank()) + labs(y = "Precision")
+
+
+large_adcal_limit_nb_recall_plot     = ggplot(large_adcal_limit_nb_dat, aes(x=function_used, y=recall)) + geom_boxplot() + theme_bw() + theme(axis.title.x = element_blank()) + labs(y = "Recall")
+
+
+large_adcal_limit_nb_time_taken_plot = ggplot(large_adcal_limit_nb_dat, aes(x=function_used, y=time_taken)) + scale_y_continuous(trans='log10') + geom_boxplot() + theme_bw() + theme(axis.title.x = element_blank()) + labs(y = "Time Taken (s)")
+
+
+
+ggsave(large_adcal_limit_nb_precision_plot,  file="plots/large_adcal_limit_nb_precision_plot.pdf", width=2.6, height=3, device=cairo_pdf)
+ggsave(large_adcal_limit_nb_recall_plot,     file="plots/large_adcal_limit_nb_recall_plot.pdf", width=2.6, height=3, device=cairo_pdf)
+ggsave(large_adcal_limit_nb_time_taken_plot, file="plots/large_adcal_limit_nb_time_plot.pdf", width=2.6, height=3, device=cairo_pdf)