added plot_data_na.R for plotting non-asthmatics fp adults

plot_data_na.R

@@ -0,0 +1,60 @@
+#!/usr/bin/Rscript   
+getwd()
+setwd("~/git/mosaic_2020/")
+getwd()
+############################################################
+# TASK: boxplots at T1
+# FIXME: currently not rendering, problem with NAs for stats?
+############################################################
+
+#=============
+# Input
+#=============
+source("data_extraction_formatting_non_asthmatics.R")
+
+# check: adult variable and age variable discrepancy!
+metadata_all$mosaic[metadata_all$adult==1 & metadata_all$age<=18]
+
+#===============================
+# data assignment for plots
+#================================
+#-----------
+# npa
+#-----------
+wf_fp_npa = npa_wf[npa_wf$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$mediator == "vitd",]
+table(lf_fp_npa$mediator)
+
+#-----------
+# sam
+#-----------
+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)
+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$mediator)
+
+#-----------
+# serum
+#-----------
+wf_fp_serum = serum_wf[serum_wf$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$obesity)
+
+head(lf_fp_sam$value[lf_fp_serum$mediator == "vitd"])
+########################################################################
+