From e71a2ccd407d80410d012180fecf57dbe569194d Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Fri, 20 Nov 2020 13:15:49 +0000 Subject: [PATCH] added plot_data_na.R for plotting non-asthmatics fp adults --- plot_data_na.R | 60 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100755 plot_data_na.R diff --git a/plot_data_na.R b/plot_data_na.R new file mode 100755 index 0000000..34640a9 --- /dev/null +++ b/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"]) +######################################################################## +