diff --git a/boxplot_linear.R b/boxplot_linear.R
new file mode 100644
index 0000000..5a41b01
--- /dev/null
+++ b/boxplot_linear.R
@@ -0,0 +1,159 @@
+#!/usr/bin/Rscript   
+getwd()
+setwd("~/git/mosaic_2020/")
+getwd()
+############################################################
+# TASK: boxplots at T1
+# FIXME: currently not rendering, problem with NAs for stats?
+############################################################
+my_samples = "npa_sam_serum"
+#=============
+# Input
+#=============
+source("data_extraction_formatting.R")
+
+# check: adult variable and age variable discrepancy!
+metadata_all$mosaic[metadata_all$adult==1 & metadata_all$age<=18]
+
+#=============
+# Output:
+#=============
+outfile_bp = paste0("boxplots_linear_", my_samples, ".pdf")
+output_boxplot = paste0(outdir_plots, outfile_bp); output_boxplot
+
+#===============================
+# data assignment for plots
+#================================
+#wf_fp_npa = npa_wf[npa_wf$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$timepoint)
+lf_fp_npa$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$mediator == "vitd",]
+
+
+#wf_fp_sam = samm_wf[samm_wf$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$timepoint)
+lf_fp_sam$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$mediator == "vitd",]
+
+
+#wf_fp_serum = serum_wf[serum_wf$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$timepoint)
+lf_fp_serum$obesity = as.factor(lf_fp_serum$obesity)
+
+########################################################################
+cat("Output plots will be in:", output_boxplot)
+pdf(output_boxplot, width = 20, height = 15)
+
+#=======================================================================
+#                         NPA
+#=======================================================================
+if (is.factor(lf_fp_npa$timepoint) && is.factor(lf_fp_npa$timepoint)){
+  cat ("PASS: required groups are factors")
+}
+#------------------------------------------
+title_npa_linear = "Boxplot: NPA (Linear)"
+#-----------------------------------------
+bxp_npa_linear <- ggboxplot(lf_fp_npa, x = "timepoint", y = "value", 
+                            color = "obesity", palette = c("#00BFC4", "#F8766D")) +
+  facet_wrap(~mediator, nrow = 7, ncol = 5, scales = "free_y", shrink = T)+
+  #scale_y_log10() + 
+  theme(axis.text.x = element_text(size = 15)
+        , axis.text.y = element_text(size = 15
+                                     , angle = 0
+                                     , hjust = 1
+                                     , vjust = 0)
+        , axis.title.x = element_text(size = 15)
+        , axis.title.y = element_text(size = 15)
+        , plot.title = element_text(size = 20, hjust = 0.5)
+        , strip.text.x = element_text(size = 15, colour = "black")
+        , legend.title = element_text(color = "black", size = 20)
+        , legend.text = element_text(size = 15)
+        , legend.direction = "horizontal") +
+  labs(title = title_npa_linear
+       , x = ""
+       , y = "Levels")
+
+bxp_npa_linear
+
+
+#=======================================================================
+#                         SAM
+#=======================================================================
+if (is.factor(lf_fp_sam$timepoint) && is.factor(lf_fp_sam$timepoint)){
+  cat ("PASS: required groups are factors")
+}
+
+#------------------------------------------
+title_sam_linear = "Boxplot: sam (Linear)"
+#-----------------------------------------
+bxp_sam_linear <- ggboxplot(lf_fp_sam, x = "timepoint", y = "value", 
+                 color = "obesity", palette = c("#00BFC4", "#F8766D")) +
+  facet_wrap(~mediator, nrow = 7, ncol = 5, scales = "free_y", shrink = T)+
+  #scale_y_log10() + 
+  theme(axis.text.x = element_text(size = 15)
+                          , axis.text.y = element_text(size = 15
+                                                       , angle = 0
+                                                       , hjust = 1
+                                                       , vjust = 0)
+                          , axis.title.x = element_text(size = 15)
+                          , axis.title.y = element_text(size = 15)
+                          , plot.title = element_text(size = 20, hjust = 0.5)
+                          , strip.text.x = element_text(size = 15, colour = "black")
+                          , legend.title = element_text(color = "black", size = 20)
+                          , legend.text = element_text(size = 15)
+                          , legend.direction = "horizontal") +
+  labs(title = title_sam_linear
+       , x = ""
+       , y = "Levels")
+
+bxp_sam_linear
+
+#=======================================================================
+#                        SERUM
+#=======================================================================
+if (is.factor(lf_fp_serum$timepoint) && is.factor(lf_fp_serum$timepoint)){
+  cat ("PASS: required groups are factors")
+}
+
+table(lf_fp_serum$mediator)
+
+#------------------------------------------
+title_serum_linear = "Boxplot: serum (Linear)"
+#-----------------------------------------
+bxp_serum_linear <- ggboxplot(lf_fp_serum, x = "timepoint", y = "value", 
+                              color = "obesity", palette = c("#00BFC4", "#F8766D")) +
+  facet_wrap(~mediator, nrow = 7, ncol = 5, scales = "free_y", shrink = T)+
+  #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_text(size = 15)
+        , axis.title.y = element_text(size = 15)
+        , 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_serum_linear
+       , x = ""
+       , y = "Levels")
+
+bxp_serum_linear
+
+#==========================================================================
+dev.off()
+############################################################################
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