From 8015dd4d6a4c45a8c871fa76934ebd8a8f2561f3 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Fri, 30 Oct 2020 20:56:15 +0000
Subject: [PATCH] fixed colours as well

---
 boxplot_with_stats.R | 101 +++++++++++++++++++++++++++++++++++++++----
 1 file changed, 92 insertions(+), 9 deletions(-)

diff --git a/boxplot_with_stats.R b/boxplot_with_stats.R
index 7736230..039534e 100755
--- a/boxplot_with_stats.R
+++ b/boxplot_with_stats.R
@@ -9,7 +9,7 @@ getwd()
 #=============
 # Input
 #=============
-#source("boxplot_linear.R")
+source("boxplot_linear.R")
 #######################################################
 med_names = c("eotaxin3", "il12p70", "itac", "il13")
 lf_test = lf_fp_npa[lf_fp_npa$mediator%in%med_names,]
@@ -73,7 +73,8 @@ stat_npa3 <- lf_test %>%
   group_by(timepoint, mediator) %>%
   wilcox_test(value ~ obesity, paired = F) %>%
   add_significance("p")
-stat_npa3 
+stat_npa3
+stat_npa3$p_format = round(stat_npa3$p, 3)
 
 stat_npa3 <- stat_npa3 %>%
   add_xy_position(x = "timepoint", dodge = 0.8)
@@ -108,6 +109,8 @@ head(stat_npa3_v2); head(stat_npa3)
 p3 = ggplot(lf_test)+ geom_boxplot(aes(x = timepoint
                                       , y = value
                                       , color = obesity))+
+  scale_colour_manual(values=c("blue", "red")) + 
+  
   theme(axis.text.x = element_text(size = 15)
         , axis.text.y = element_text(size = 15
                                      , angle = 0
@@ -115,24 +118,25 @@ p3 = ggplot(lf_test)+ geom_boxplot(aes(x = timepoint
                                      , vjust = 0)
         , axis.title.x = element_blank()
         , axis.title.y = element_blank()
-        , legend.position = "none"
+        , strip.text.x = element_text(size = 20)
+        , legend.position = "top" 
+        , legend.title = element_text(color = "black", size = 20)
+        , legend.text = element_text(size = 15)
         , plot.subtitle = element_text(size = 20, hjust = 0.5)
         , plot.title = element_text(size = 20, hjust = 0.5)) +
   labs(title ="NPA")+
-  #facet_wrap(~mediator, scales = "free")
-
-p3_build = ggbuild(p3)  
-  
+  facet_wrap(~mediator, scales = "free", nrow = 2, ncol = 2)
+#p3
 p4 = p3 + stat_pvalue_manual(stat_npa3_v2
                              , y.position = "my_y_pos"
                              #, y.position = 50
-                             , label = "{p} {p.signif}"
+                             , label = "{p_format} {p.signif}"
                              , hide.ns=T
                              , tip.length = 0)+
   scale_y_continuous(expand = expansion(mult = c(0.05, 0.25)))
 
 p4
-#========================================
+#=======================================
 p3_build = ggplot_build(p3)
 p3_build$layout$panel_scales_y
 
@@ -150,3 +154,82 @@ get_facet_ymax <- function (x){
 }
 
 y_max_l = get_facet_ymax(p3_build); y_max_l
+#===============================================
+# facet wrap on actual data
+pdf("boxplot_stats.pdf", width = 20, height = 15)
+#=======
+# facet
+#=======
+#--------
+# wilcox stats
+#--------
+stat_npa3 <- lf_fp_npa %>%
+  group_by(timepoint, mediator) %>%
+  wilcox_test(value ~ obesity, paired = F) %>%
+  add_significance("p")
+stat_npa3 
+stat_npa3$p_format = round(stat_npa3$p, 3)
+
+stat_npa3 <- stat_npa3 %>%
+  add_xy_position(x = "timepoint", dodge = 0.8)
+head(stat_npa3)
+
+#--------
+# summary stats
+#--------
+my_summary = lf_fp_npa %>%
+  group_by(timepoint, mediator) %>%
+  get_summary_stats(value)
+my_summary
+my_max_df = subset(my_summary
+                   , select = c("mediator", "timepoint"
+                                #, "obesity"
+                                , "max"))
+
+head(my_max_df); head(stat_npa3)
+
+#-----------------------------
+# merge my_max and stat_npa3
+#-----------------------------
+head(my_max_df)
+merging_cols = intersect(names(stat_npa3), names(my_max_df)); merging_cols
+
+stat_npa3_v2 = merge(stat_npa3, my_max_df, by = merging_cols, all.x = T)
+stat_npa3_v2$my_y_pos = (stat_npa3_v2$max)*1.2
+stat_npa3_v2$my_y_pos
+
+head(stat_npa3_v2); head(stat_npa3)
+
+
+p3 = ggplot(lf_fp_npa)+ geom_boxplot(aes(x = timepoint
+                                         , y = value
+                                         , color = obesity))+
+  scale_colour_manual(values=c("blue", "red")) + 
+  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_blank()
+        , axis.title.y = element_blank()
+        , strip.text.x = element_text(size = 20)
+        , legend.position = "top" 
+        , legend.title = element_text(color = "black", size = 20)
+        , legend.text = element_text(size = 15)
+        , plot.subtitle = element_text(size = 20, hjust = 0.5)
+        , plot.title = element_text(size = 20, hjust = 0.5)) +
+  labs(title ="NPA")+
+  facet_wrap(~mediator, scales = "free", nrow = 5, ncol = 7)
+#p3
+p4 = p3 + stat_pvalue_manual(stat_npa3_v2
+                             , y.position = "my_y_pos"
+                             #, y.position = 50
+                             , label = "{p_format} {p.signif}"
+                             , hide.ns=T
+                             , tip.length = 0) #+
+  #scale_y_continuous(expand = expansion(mult = c(0.05, 0.25)))
+
+p4
+dev.off()