diff --git a/boxplot_stat_all.R b/boxplot_stat_all.R
old mode 100644
new mode 100755
index b271c1d..5288fb6
--- a/boxplot_stat_all.R
+++ b/boxplot_stat_all.R
@@ -3,19 +3,31 @@ getwd()
 setwd("~/git/mosaic_2020/")
 getwd()
 ###############################################################
+#=============
+# Input
+#=============
 source("boxplot_stat_function.R")
 source("plot_data.R")
+
 #=============
-# Output:
+# Output
 #=============
 outfile_bp = paste0("boxplots_stats_all", ".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
-#===========================
+#-------------
 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 = doMyPlots(lf_fp_npa)
 npa_plot = ggpubr::ggarrange(plotlist = plots_npa
                              , align = "hv"
@@ -24,36 +36,64 @@ npa_plot = ggpubr::ggarrange(plotlist = plots_npa
                              , 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("Mosaic data\nFlu positive adults (n=133)"
+                , 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))
+                                   , 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"
-plots_sam = doMyPlots(lf_fp_sam)
-sam_plot = ggpubr::ggarrange(plotlist = plots_sam
-                             , align = "hv"
-                             , ncol = 7
-                             , nrow = 5
-                             , common.legend = T)
+#-------------
+#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("Mosaic data\nFlu positive adults (n=133)"
-                                                      , 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
+#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 
-#===========================
+#-------------
 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 = doMyPlots(lf_fp_serum)
 serum_plot = ggpubr::ggarrange(plotlist = plots_serum
                                , align = "hv"
@@ -62,10 +102,20 @@ serum_plot = ggpubr::ggarrange(plotlist = plots_serum
                                , 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("Mosaic data\nFlu positive adults (n=133)"
+                                   , 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))
+                                                        , 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_stat_function.R b/boxplot_stat_function.R
old mode 100644
new mode 100755
diff --git a/boxplot_stat_test.R b/boxplot_stat_function_test.R
old mode 100644
new mode 100755
similarity index 61%
rename from boxplot_stat_test.R
rename to boxplot_stat_function_test.R
index 4866521..f9a86fd
--- a/boxplot_stat_test.R
+++ b/boxplot_stat_function_test.R
@@ -11,6 +11,7 @@ source("plot_data.R")
 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,]
 
 foo = doMyPlots(lf_fp_sam2)
 
@@ -23,11 +24,19 @@ pdf(output_boxplot_stats, width=22, height=16)
 
 #baz=cowplot::plot_grid(plotlist=foo, align = 'hv', ncol=2, nrow=2)
 foo_annot = annotate_figure(foo
-                            , top = text_grob(my_sample_name, color = "blue", face = "bold", size = 14)
+                            , top = text_grob(my_sample_name
+                                              , color = "blue"
+                                              , face = "bold"
+                                              , size = 14)
                             , bottom = text_grob("Mosaic data\nFlu positive adults (n=133)"
                                                  , color = "blue"
-                                                 , hjust = 1, x = 0.98, face = "italic", size = 10)
-                            , left = text_grob("Levels (pg/ml)", color = "black", rot = 90, size = 18)
+                                                 , hjust = 1, x = 0.98
+                                                 , face = "italic"
+                                                 , size = 10)
+                            , left = text_grob("Levels (pg/ml)"
+                                               , color = "black"
+                                               , rot = 90
+                                               , size = 18)
 )
 foo_annot
 dev.off()
diff --git a/boxplot_with_stats.R b/boxplot_with_stats.R
old mode 100644
new mode 100755
diff --git a/plot_data.R b/plot_data.R
old mode 100644
new mode 100755
index 4df2c41..5d34538
--- a/plot_data.R
+++ b/plot_data.R
@@ -6,7 +6,7 @@ getwd()
 # TASK: boxplots at T1
 # FIXME: currently not rendering, problem with NAs for stats?
 ############################################################
-my_samples = "npa_sam_serum"
+
 #=============
 # Input
 #=============
@@ -15,12 +15,6 @@ source("data_extraction_formatting.R")
 # check: adult variable and age variable discrepancy!
 metadata_all$mosaic[metadata_all$adult==1 & metadata_all$age<=18]
 
-#=============
-# Output:
-#=============
-outfile_bp = paste0("boxplots_linear_", my_samples, ".pdf")
-output_boxplot = paste0(outdir_plots, outfile_bp); output_boxplot
-
 #===============================
 # data assignment for plots
 #================================
@@ -36,6 +30,7 @@ lf_fp_npa$obesity = as.factor(lf_fp_npa$obesity)
 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",]
+table(lf_fp_npa$mediator)
 
 #-----------
 # sam
@@ -49,6 +44,7 @@ lf_fp_sam$obesity = as.factor(lf_fp_sam$obesity)
 table(lf_fp_sam$mediator)
 head(lf_fp_sam$value[lf_fp_sam$mediator == "vitd"])
 lf_fp_sam = lf_fp_sam[!lf_fp_sam$mediator == "vitd",]
+table(lf_fp_sam$mediator)
 
 #-----------
 # serum
@@ -59,4 +55,5 @@ lf_fp_serum$timepoint = paste0("t", lf_fp_serum$timepoint)
 lf_fp_serum$timepoint = as.factor(lf_fp_serum$timepoint)
 lf_fp_serum$obesity = as.factor(lf_fp_serum$obesity)
 
+head(lf_fp_sam$value[lf_fp_serum$mediator == "vitd"])
 ########################################################################
\ No newline at end of file