From 6575fc7abab58057d2094c633033cfa9cd5176f7 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Sat, 31 Oct 2020 19:52:18 +0000
Subject: [PATCH] updating the function

---
 boxplot_stat_function.R | 68 ++++++++++++++++++++++-------------------
 boxplot_with_stats.R    | 18 ++++++-----
 2 files changed, 48 insertions(+), 38 deletions(-)
 mode change 100755 => 100644 boxplot_with_stats.R

diff --git a/boxplot_stat_function.R b/boxplot_stat_function.R
index 43b994b..dc209c6 100644
--- a/boxplot_stat_function.R
+++ b/boxplot_stat_function.R
@@ -3,8 +3,7 @@ getwd()
 setwd("~/git/mosaic_2020/")
 getwd()
 ############################################################
-# TASK: boxplots at T1
-# FIXME: currently not rendering, problem with NAs for stats?
+# TASK: boxplots with stats
 ############################################################
 doMyPlots <- function(x, title  = "TEST") {
     mediators = levels(as.factor(x$mediator))
@@ -18,30 +17,30 @@ doMyPlots <- function(x, title  = "TEST") {
       max_y = max(single$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"))
+                     #, palette = c("blue", "red")
+                     , 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")
-      
+      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_blank()
+            , legend.position = "none"
+            , plot.subtitle = element_text(size = 20, hjust = 0.5)
+            , plot.title = element_text(size = 20, hjust = 0.5)) +
+        labs(title = i)
+      #--------
       # stats
+      #---------
       stat_npa2 <- single %>%
         group_by(timepoint, mediator) %>%
         wilcox_test(value ~ obesity, paired = F) %>%
@@ -51,15 +50,16 @@ doMyPlots <- function(x, title  = "TEST") {
       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
+                                   #, 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)))
+                                   , tip.length = 0)+
+        scale_y_continuous(expand = expansion(mult = c(0.05, 0.25))) +
+        scale_x_discrete()
       
       plots[[i]] <- p2
+      
     }
     return(plots)
 
@@ -70,26 +70,32 @@ doMyPlots <- function(x, title  = "TEST") {
 # test
 #============
 source("boxplot_linear.R")
-
 #=============
 # Output:
 #=============
-outfile_bp = paste0("boxplots_TEST_stats_all", ".pdf")
+outfile_bp = paste0("boxplots_TEST", ".pdf")
 output_boxplot_stats = paste0(outdir_plots, outfile_bp); output_boxplot_stats
-
-pdf(output_boxplot_stats, width=32, height=18)
+pdf(output_boxplot_stats, width=22, height=16)
 
 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=cowplot::plot_grid(plotlist=foo, align = 'hv', ncol=2, nrow=2)
 baz
+dev.off()
 
+#=========================
 # entire sample_type data
-#bar=doMyPlots(lf_fp_npa)
+#=========================
+my_sample_type = "NPA"
+outfile_bp = paste0("boxplots_stats_", my_sample_type, ".pdf")
+output_boxplot_stats = paste0(outdir_plots, outfile_bp); output_boxplot_stats
+pdf(output_boxplot_stats, width=22, height=16)
+
+bar=doMyPlots(lf_fp_npa)
 #bang=cowplot::plot_grid(plotlist=bar, align = 'hv', ncol=7, nrow=5)
 #bang
 
-dev.off()
+
+dev.off()
\ No newline at end of file
diff --git a/boxplot_with_stats.R b/boxplot_with_stats.R
old mode 100755
new mode 100644
index cf35f5d..da73758
--- a/boxplot_with_stats.R
+++ b/boxplot_with_stats.R
@@ -62,15 +62,21 @@ p2 = p2 + stat_pvalue_manual(stat_npa2
                              , hide.ns=T
                              , tip.length = 0)+
   scale_y_continuous(expand = expansion(mult = c(0.05, 0.25))) +
-  scale_x_discrete()
-
+  
 plots[[i]] <- p2
 
 }
-
+#============================
+# combine: cowplot_plot_grid
+#============================
 #cowplot::plot_grid(plotlist=plots, align = 'hv', ncol=2, nrow=2)
+pdf("test.pdf", width = 22, height = 16)
+cowplot::plot_grid(plotlist=plots, align = 'hv', ncol=7, nrow=5)
+dev.off()
+#===========================
+# combine: ggpubr::ggarrange
+#===========================
 pdf("test2.pdf", width = 22, height = 16)
-
 npa_plot<- ggpubr::ggarrange(plotlist = plots, align = "hv"
                              , ncol = 7
                              , nrow = 5
@@ -86,9 +92,7 @@ annotate_figure(npa_plot,
                 #fig.lab = "Figure 1", fig.lab.face = "bold"
                 )
 
-pdf("test.pdf", width = 22, height = 16)
-cowplot::plot_grid(plotlist=plots, align = 'hv', ncol=7, nrow=5)
-dev.off()
+
 ##################################################################
 #=======
 # facet