added boxplot_stat_function.R

boxplot_stat_function.R

@@ -0,0 +1,95 @@
+#!/usr/bin/Rscript   
+getwd()
+setwd("~/git/mosaic_2020/")
+getwd()
+############################################################
+# TASK: boxplots at T1
+# FIXME: currently not rendering, problem with NAs for stats?
+############################################################
+doMyPlots <- function(x, title  = "TEST") {
+    mediators = levels(as.factor(x$mediator))
+    
+    plots <- list()
+    
+    for (i in mediators) {
+      cat("Plotting:", i, "\n")
+      single=x[x$mediator==i,]
+      
+      max_y = max(single$value, na.rm = T)
+      cat("Plotting:", i, "max_y:", max_y, "\n")
+      
+      # boxplot
+      p2 = ggboxplot(single
+                     , x = "timepoint"
+                     , y = "value"
+                     , color = "obesity"
+                     , palette = c("#00BFC4", "#F8766D"))
+        
+      p2 = p2 +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_blank()
+                     , axis.title.y = element_
+                     , 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
+             , x = ""
+             , y = "Levels")
+      
+      # stats
+      stat_npa2 <- single %>%
+        group_by(timepoint, mediator) %>%
+        wilcox_test(value ~ obesity, paired = F) %>%
+        add_significance("p")
+      stat_npa2
+      
+      stat_npa2 <- stat_npa2 %>%
+        add_xy_position(x = "timepoint", dodge = 0.8)
+      
+      # add stats to boxplot
+      p2 = p2 + stat_pvalue_manual(stat_npa2
+                                   , y.position = max_y
+                                   , label = "{p} {p.signif}"
+                                   , hide.ns=T
+                                   , tip.length = 0) +
+        scale_y_continuous(expand = expansion(mult = c(0.05, 0.25)))
+      
+      plots[[i]] <- p2
+    }
+    return(plots)
+
+  }
+
+###############################################################
+#============
+# test
+#============
+source("boxplot_linear.R")
+
+#=============
+# Output:
+#=============
+outfile_bp = paste0("boxplots_TEST_stats_all", ".pdf")
+output_boxplot_stats = paste0(outdir_plots, outfile_bp); output_boxplot_stats
+
+pdf(output_boxplot_stats, width=32, height=18)
+
+med_names = c("eotaxin3", "il12p70", "itac", "il13")
+#lf_test = lf_fp_npa[lf_fp_npa$mediator == "il12p70",]
+lf_test = lf_fp_npa[lf_fp_npa$mediator%in%med_names,]
+
+foo=doMyPlots(lf_test)
+baz=cowplot::plot_grid(plotlist=foo, align = 'hv', ncol=2, nrow=2)
+baz
+
+# entire sample_type data
+#bar=doMyPlots(lf_fp_npa)
+#bang=cowplot::plot_grid(plotlist=bar, align = 'hv', ncol=7, nrow=5)
+#bang
+
+dev.off()