tanu/mosaic_2020
1
0
Fork 0
Code Issues Pull requests Releases Wiki Activity

added plot_data_na.R for plotting non-asthmatics fp adults

Browse source
This commit is contained in:
Tanushree Tunstall 2020-11-20 13:15:49 +00:00
parent 3b6776af24
commit e71a2ccd40
1 changed files with 60 additions and 0 deletions
Download patch file Download diff file Expand all files Collapse all files

60
plot_data_na.R Executable file
View file

@ -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"])
########################################################################