diff --git a/boxplot_stat_all.R b/boxplot_stat_all.R
index 5288fb6..a71969a 100755
--- a/boxplot_stat_all.R
+++ b/boxplot_stat_all.R
@@ -28,7 +28,7 @@ fp_npa = length(unique(lf_fp_npa$mosaic)); fp_npa
 cat("\nPlotting boxplots with stats for:", my_sample_npa
     , "\n========================================================\n")
 
-plots_npa = doMyPlots(lf_fp_npa)
+plots_npa = doMyPlotsStats(lf_fp_npa)
 npa_plot = ggpubr::ggarrange(plotlist = plots_npa
                              , align = "hv"
                              , ncol = 7
@@ -94,7 +94,7 @@ fp_serum = length(unique(lf_fp_serum$mosaic)); fp_serum
 cat("\nPlotting boxplots with stats for:", my_sample_serum
     , "\n========================================================\n")
 
-plots_serum = doMyPlots(lf_fp_serum)
+plots_serum = doMyPlotsStats(lf_fp_serum)
 serum_plot = ggpubr::ggarrange(plotlist = plots_serum
                                , align = "hv"
                                , ncol = 7
diff --git a/boxplot_stat_function.R b/boxplot_stat_function.R
index 070adf9..e8f0e1c 100755
--- a/boxplot_stat_function.R
+++ b/boxplot_stat_function.R
@@ -5,7 +5,7 @@ getwd()
 ############################################################
 # TASK: boxplots with stats
 ############################################################
-doMyPlots <- function(df) {
+doMyPlotsStats <- function(df) {
     mediators = levels(as.factor(df$mediator))
     
     plots <- list()
@@ -61,4 +61,5 @@ doMyPlots <- function(df) {
     return(plots)
   }
 
-###############################################################
\ No newline at end of file
+###############################################################
+
diff --git a/boxplot_stat_function_test.R b/boxplot_stat_function_test.R
index f9a86fd..f75f2d3 100755
--- a/boxplot_stat_function_test.R
+++ b/boxplot_stat_function_test.R
@@ -22,8 +22,16 @@ pdf(output_boxplot_stats, width=22, height=16)
 #med_names = c("eotaxin3", "il12p70", "itac", "il13")
 #lf_test = lf_fp_npa[lf_fp_npa$mediator%in%med_names,]
 
-#baz=cowplot::plot_grid(plotlist=foo, align = 'hv', ncol=2, nrow=2)
-foo_annot = annotate_figure(foo
+baz=cowplot::plot_grid(plotlist=foo, align = 'hv', ncol=2, nrow=2)
+baz
+
+sam_plot = ggpubr::ggarrange(plotlist = foo
+                             , align = "hv"
+                             , ncol = 7
+                             , nrow = 5
+                             , common.legend = T)
+sam_plot
+foo_annot = annotate_figure(sam_plot
                             , top = text_grob(my_sample_name
                                               , color = "blue"
                                               , face = "bold"
@@ -41,3 +49,80 @@ foo_annot = annotate_figure(foo
 foo_annot
 dev.off()
 ##################################################################
+# ind components of function
+my_sample_name = "SAM"
+to_remove = c("ifna2a"
+              , "il29")
+
+lf_fp_sam2 = lf_fp_sam[!lf_fp_sam$mediator%in%to_remove,]
+lf_fp_sam3 = lf_fp_sam[lf_fp_sam$mediator%in%to_remove,]
+
+df_test = lf_fp_sam3
+df_test = lf_fp_sam2
+table(df_test$mediator)
+
+p = ggplot(df_test)+ geom_boxplot(aes(x = timepoint
+                                     , y = value
+                                     , color = obesity
+                                     #, palette = c("#00BFC4", "#F8766D")
+))+
+  scale_colour_manual(values=c("#00BFC4", "#F8766D")) + 
+  theme(axis.text.x = element_text(size = 15)
+        , axis.text.y = element_text(size = 15
+                                     , angle = 0
+                                     , hjust = 1
+                                     , vjust = 0)
+        , axis.title.x = element_blank()
+        , axis.title.y = element_blank()
+        , legend.position = "none"
+        , plot.subtitle = element_text(size = 20, hjust = 0.5)
+        , plot.title = element_text(size = 20, hjust = 0.5)) +
+  labs(title = "TEST")
+p
+
+#--------
+# stats
+#---------
+to_remove = c("ifna2a"
+              , "il29")
+lf_fp_sam3 = lf_fp_sam[lf_fp_sam$mediator%in%to_remove,]
+
+lf_fp_sam4 = lf_fp_sam3[lf_fp_sam3$timepoint == "t3",]
+table(lf_fp_sam4$timepoint)
+
+wilcox_test(value~obesity, data = lf_fp_sam4)
+
+table(lf_fp_sam3$mediator, lf_fp_sam3$timepoint)
+time = c("t3")
+lf_fp_sam3 = lf_fp_sam3[!lf_fp_sam3$timepoint%in%time,]
+table(lf_fp_sam3$mediator, lf_fp_sam3$timepoint)
+
+med = c("il29")
+time2 = c("t2")
+
+lf_fp_sam3 = lf_fp_sam3[!lf_fp_sam3$mediator%in%med && lf_fp_sam3$timepoint%in%time2,]
+table(lf_fp_sam3$mediator, lf_fp_sam3$timepoint)
+
+df_test = lf_fp_sam3
+
+
+table(df_test$mediator)
+
+
+stat_df <- df_test %>%
+  group_by(timepoint, mediator) %>%
+  wilcox_test(value ~ obesity, paired = F) %>%
+  add_significance("p")
+stat_df$p_format = round(stat_df$p, digits = 3)
+
+
+stat_df <- stat_df %>%
+  add_xy_position(x = "timepoint", dodge = 0.8)
+p2 = p + stat_pvalue_manual(stat_df
+                            #, y.position = max_y
+                            , label = "{p_format} {p.signif}"
+                            , hide.ns = T
+                            , tip.length = 0)+
+  scale_y_continuous(expand = expansion(mult = c(0.05, 0.25)))
+
+p2
diff --git a/boxplot_stat_log.R b/boxplot_stat_log.R
new file mode 100644
index 0000000..0953113
--- /dev/null
+++ b/boxplot_stat_log.R
@@ -0,0 +1,153 @@
+#!/usr/bin/Rscript   
+getwd()
+setwd("~/git/mosaic_2020/")
+getwd()
+###############################################################
+#=============
+# Input
+#=============
+source("boxplot_stat_function.R")
+source("plot_data.R")
+
+#=============
+# Output
+#=============
+outfile_bp = paste0("boxplots_stats_npa_serum_LOG", ".pdf")
+output_boxplot_stats = paste0(outdir_plots, outfile_bp); output_boxplot_stats
+pdf(output_boxplot_stats, width=22, height=16)
+###############################################################
+#===============================
+# data assignment for plots
+#===============================
+#----------------------------------------
+#-------
+# NPA
+#-------
+# vl data juggling with 0!
+vl_temp_fix = lf_fp_npa[lf_fp_npa$mediator=="vl_pfu_ul",]
+vl_temp_fix$value[1:20]
+vl_temp_fix$value[vl_temp_fix$value == 0] <- 1
+vl_temp_fix$value[1:20]
+
+orig_nrow = nrow(lf_fp_npa); orig_nrow; table(lf_fp_npa$mediator)
+lf_fp_npa = lf_fp_npa[!lf_fp_npa$mediator=="vl_pfu_ul",]
+temp_nrow = nrow(lf_fp_npa); temp_nrow; table(lf_fp_npa$mediator)
+
+# add vl_temp_fix back
+lf_fp_npa = rbind(lf_fp_npa, vl_temp_fix)
+revised_nrow = nrow(lf_fp_npa); revised_nrow
+
+orig_nrow == revised_nrow
+
+head(lf_fp_npa$value)
+
+# log all values and reassign
+lf_fp_npa$value = log10(lf_fp_npa$value)
+head(lf_fp_npa$value)
+vl_temp_fix2 = lf_fp_npa[lf_fp_npa$mediator=="vl_pfu_ul",]
+vl_temp_fix2$value[1:20]
+
+#------------------------------------------
+my_sample_npa = "NPA"
+fp_npa = length(unique(lf_fp_npa$mosaic)); fp_npa
+
+cat("\nPlotting boxplots with stats for:", my_sample_npa
+    , "\n========================================================\n")
+
+plots_npa = doMyPlotsStats(lf_fp_npa)
+npa_plot = ggpubr::ggarrange(plotlist = plots_npa
+                             , align = "hv"
+                             , ncol = 7
+                             , nrow = 5
+                             , common.legend = T)
+#npa_plot
+npa_plot_annot = annotate_figure(npa_plot
+                , top = text_grob(my_sample_npa
+                                  , color = "blue"
+                                  , face = "bold"
+                                  , size = 14)
+                , bottom = text_grob(paste0("Mosaic data\nFlu positive adults (n=", fp_npa, ")")
+                                   , color = "blue"
+                                   , hjust = 1
+                                   , x = 0.98
+                                   , face = "italic"
+                                   , size = 10)
+                , left = text_grob("Levels (pg/ml)"
+                                   , color = "black"
+                                   , rot = 90
+                                   , size = 18))
+npa_plot_annot
+#dev.off()
+#-------------
+# SAM
+#-------------
+#my_sample_sam = "SAM"
+#fp_sam = length(unique(lf_fp_sam$mosaic)); fp_sam
+
+#cat("\nPlotting boxplots with stats for:", my_sample_sam
+#    , "\n========================================================\n")
+
+#plots_sam = doMyPlots(lf_fp_sam)
+#sam_plot = ggpubr::ggarrange(plotlist = plots_sam
+#                             , align = "hv"
+#                             , ncol = 7
+#                             , nrow = 5
+#                             , common.legend = T)
+#sam_plot
+#sam_plot_annot = annotate_figure(sam_plot
+#                                 , top = text_grob(my_sample_sam
+#                                                   , color = "blue"
+#                                                   , face = "bold"
+#                                                   , size = 14)
+#                                 , bottom = text_grob(paste0("Mosaic data\nFlu positive adults (n=", fp_sam, ")")
+#                                                      , color = "blue"
+#                                                      , hjust = 1
+#                                                      , x = 0.98
+#                                                      , face = "italic"
+#                                                      , size = 10)
+#                                 , left = text_grob("Levels (pg/ml)"
+#                                                    , color = "black"
+#                                                    , rot = 90
+#                                                    , size = 18))
+#sam_plot_annot
+#dev.off()
+#------------------------------------------
+#-------------
+# SERUM 
+#-------------
+head(lf_fp_serum$value)
+# reassign 
+lf_fp_serum$value = log10(lf_fp_serum$value)
+head(lf_fp_serum$value)
+
+my_sample_serum = "serum"
+fp_serum = length(unique(lf_fp_serum$mosaic)); fp_serum
+
+cat("\nPlotting boxplots with stats for:", my_sample_serum
+    , "\n========================================================\n")
+
+plots_serum = doMyPlotsStats(lf_fp_serum)
+serum_plot = ggpubr::ggarrange(plotlist = plots_serum
+                               , align = "hv"
+                               , ncol = 7
+                               , nrow = 5
+                               , common.legend = T)
+#serum_plot
+serum_plot_annot = annotate_figure(serum_plot
+                                   , top = text_grob(my_sample_serum
+                                                     , color = "blue"
+                                                     , face = "bold"
+                                                     , size = 14)
+                                   , bottom = text_grob(paste0("Mosaic data\nFlu positive adults (n=", fp_serum, ")")
+                                                        , color = "blue"
+                                                        , hjust = 1
+                                                        , x = 0.98
+                                                        , face = "italic"
+                                                        , size = 10)
+                                   , left = text_grob("Levels (pg/ml)"
+                                                      , color = "black"
+                                                      , rot = 90
+                                                      , size = 18))
+serum_plot_annot
+dev.off()
+###############################################################
diff --git a/boxplot_with_stats_test.R b/boxplot_with_stats_test.R
index da73758..f513cc2 100755
--- a/boxplot_with_stats_test.R
+++ b/boxplot_with_stats_test.R
@@ -9,7 +9,7 @@ getwd()
 #=============
 # Input
 #=============
-source("boxplot_linear.R")
+source("plot_data.R")
 #######################################################
 med_names = c("eotaxin3", "il12p70", "itac", "il13")
 lf_test = lf_fp_npa[lf_fp_npa$mediator%in%med_names,]
diff --git a/plot_data.R b/plot_data.R
index 5d34538..a1150ca 100755
--- a/plot_data.R
+++ b/plot_data.R
@@ -21,7 +21,7 @@ metadata_all$mosaic[metadata_all$adult==1 & metadata_all$age<=18]
 #-----------
 # npa
 #-----------
-#wf_fp_npa = npa_wf[npa_wf$flustat == 1,]
+wf_fp_npa = npa_wf[npa_wf$flustat == 1,]
 lf_fp_npa = npa_lf[npa_lf$flustat == 1,]
 lf_fp_npa$timepoint = paste0("t", lf_fp_npa$timepoint)
 lf_fp_npa$timepoint = as.factor(lf_fp_npa$timepoint)
@@ -35,7 +35,7 @@ table(lf_fp_npa$mediator)
 #-----------
 # sam
 #-----------
-#wf_fp_sam = samm_wf[samm_wf$flustat == 1,]
+wf_fp_sam = sam_wf[sam_wf$flustat == 1,]
 lf_fp_sam = sam_lf[sam_lf$flustat == 1,]
 lf_fp_sam$timepoint = paste0("t", lf_fp_sam$timepoint)
 lf_fp_sam$timepoint = as.factor(lf_fp_sam$timepoint)
@@ -49,7 +49,7 @@ table(lf_fp_sam$mediator)
 #-----------
 # serum
 #-----------
-#wf_fp_serum = serum_wf[serum_wf$flustat == 1,]
+wf_fp_serum = serum_wf[serum_wf$flustat == 1,]
 lf_fp_serum = serum_lf[serum_lf$flustat == 1,]
 lf_fp_serum$timepoint = paste0("t", lf_fp_serum$timepoint)
 lf_fp_serum$timepoint = as.factor(lf_fp_serum$timepoint)