From 7463f9ac1c8986da07ee6ae1bbc29632badbc048 Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Thu, 29 Oct 2020 18:56:31 +0000 Subject: [PATCH] ploting npa before sam and serum for boxplots --- boxplot.R | 144 ++++++++++++++++++++++++------------------------------ 1 file changed, 63 insertions(+), 81 deletions(-) diff --git a/boxplot.R b/boxplot.R index 035ea4d..acf827d 100644 --- a/boxplot.R +++ b/boxplot.R @@ -46,6 +46,68 @@ lf_fp_serum$obesity = as.factor(lf_fp_serum$obesity) cat("Output plots will be in:", output_boxplot) pdf(output_boxplot, width = 20, height = 15) +#======================================================================= +# NPA +#======================================================================= +if (is.factor(lf_fp_npa$timepoint) && is.factor(lf_fp_npa$timepoint)){ + cat ("PASS: required groups are factors") +} + +table(lf_fp_npa$mediator) +head(lf_fp_npa$value[lf_fp_npa$mediator == "vitd"]) +lf_fp_npa = lf_fp_npa[!lf_fp_npa$mediator == "vitd",] + +#------------------------------------------ +title_npa_linear = "Boxplot: NPA (Linear)" +#----------------------------------------- +bxp_npa_linear <- ggboxplot(lf_fp_npa, x = "timepoint", y = "value", + color = "obesity", palette = c("#00BFC4", "#F8766D")) + + facet_wrap(~mediator, nrow = 7, ncol = 5, scales = "free_y", shrink = T)+ + #scale_y_log10() + + theme(axis.text.x = element_text(size = 15) + , axis.text.y = element_text(size = 15 + , angle = 0 + , hjust = 1 + , vjust = 0) + , axis.title.x = element_text(size = 15) + , axis.title.y = element_text(size = 15) + , plot.title = element_text(size = 20, hjust = 0.5) + , strip.text.x = element_text(size = 15, colour = "black") + , legend.title = element_text(color = "black", size = 20) + , legend.text = element_text(size = 15) + , legend.direction = "horizontal") + + labs(title = title_npa_linear + , x = "" + , y = "Levels") + +bxp_npa_linear + +#------------------------------------ +title_npa_log = "Boxplot: NPA (Log)" +#----------------------------------- + +bxp_npa_log <- ggboxplot(lf_fp_npa, x = "timepoint", y = "value", + color = "obesity", palette = c("#00BFC4", "#F8766D")) + + facet_wrap(~mediator, nrow = 7, ncol = 5, scales = "free_y", shrink = F)+ + scale_y_log10() + + theme(axis.text.x = element_text(size = 15) + , axis.text.y = element_text(size = 15 + , angle = 0 + , hjust = 1 + , vjust = 0) + , axis.title.x = element_text(size = 15) + , axis.title.y = element_text(size = 15) + , plot.title = element_text(size = 20, hjust = 0.5) + , strip.text.x = element_text(size = 15, colour = "black") + , legend.title = element_text(color = "black", size = 20) + , legend.text = element_text(size = 15) + , legend.direction = "horizontal") + + labs(title = title_npa_log + , x = "" + , y = "Levels (Log)") + +bxp_npa_log + #======================================================================= # SAM #======================================================================= @@ -164,87 +226,7 @@ bxp_serum_log <- ggboxplot(lf_fp_serum, x = "timepoint", y = "value", , x = "" , y = "Levels (Log)") -bxp_serum_log -#======================================================================= -# NPA -#======================================================================= -if (is.factor(lf_fp_npa$timepoint) && is.factor(lf_fp_npa$timepoint)){ - cat ("PASS: required groups are factors") -} +bxp_serum_log -table(lf_fp_npa$mediator) -head(lf_fp_npa$value[lf_fp_npa$mediator == "vitd"]) -lf_fp_npa = lf_fp_npa[!lf_fp_npa$mediator == "vitd",] - -#------------------------------------------ -title_npa_linear = "Boxplot: NPA (Linear)" -#----------------------------------------- -bxp_npa_linear <- ggboxplot(lf_fp_npa, x = "timepoint", y = "value", - color = "obesity", palette = c("#00BFC4", "#F8766D")) + - facet_wrap(~mediator, nrow = 7, ncol = 5, scales = "free_y", shrink = T)+ - #scale_y_log10() + - theme(axis.text.x = element_text(size = 15) - , axis.text.y = element_text(size = 15 - , angle = 0 - , hjust = 1 - , vjust = 0) - , axis.title.x = element_text(size = 15) - , axis.title.y = element_text(size = 15) - , plot.title = element_text(size = 20, hjust = 0.5) - , strip.text.x = element_text(size = 15, colour = "black") - , legend.title = element_text(color = "black", size = 20) - , legend.text = element_text(size = 15) - , legend.direction = "horizontal") + - labs(title = title_npa_linear - , x = "" - , y = "Levels") - -bxp_npa_linear - -#------------------------------------ -title_npa_log = "Boxplot: NPA (Log)" -#----------------------------------- - -bxp_npa_log <- ggboxplot(lf_fp_npa, x = "timepoint", y = "value", - color = "obesity", palette = c("#00BFC4", "#F8766D")) + - facet_wrap(~mediator, nrow = 7, ncol = 5, scales = "free_y", shrink = F)+ - scale_y_log10() + - theme(axis.text.x = element_text(size = 15) - , axis.text.y = element_text(size = 15 - , angle = 0 - , hjust = 1 - , vjust = 0) - , axis.title.x = element_text(size = 15) - , axis.title.y = element_text(size = 15) - , plot.title = element_text(size = 20, hjust = 0.5) - , strip.text.x = element_text(size = 15, colour = "black") - , legend.title = element_text(color = "black", size = 20) - , legend.text = element_text(size = 15) - , legend.direction = "horizontal") + - labs(title = title_npa_log - , x = "" - , y = "Levels (Log)") - -bxp_npa_log dev.off() #========================================================================== -#------------------------------------ -title_npa_log_stats = "Boxplot: NPA (Log) + stats" -#----------------------------------- -stat.test <- lf_fp_npa %>% - group_by(timepoint, mediator) %>% - wilcox_test(value ~ obesity, paired = F) %>% - add_significance("p") -stat.test - -stat.test <- stat.test %>% - add_xy_position(x = "timepoint", dodge = 0.8) - - -bxp_npa_linear + stat_pvalue_manual(stat.test, label = "p.signif", tip.length = 0) - -bxp_npa_log + stat_pvalue_manual(stat.test, label = "p.signif", tip.length = 0) - - - -dev.off() \ No newline at end of file