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added and moved plot_data for non-asthmatics and non-severe analysis

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Tanushree Tunstall 2020-12-07 16:55:17 +00:00
parent c3b1ba9a0e
commit 3338de800a
2 changed files with 117 additions and 0 deletions
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59
plot_data_na.R Executable file
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#!/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")
source("data_extraction_mediators.R")
#===============================
# data assignment for plots
#================================
#-----------
# npa
#-----------
wf_fp_npa = npa_wf[npa_wf$asthma == 0,]
lf_fp_npa = npa_lf[npa_lf$asthma == 0,]
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$mediator)
#-----------
# sam
#-----------
wf_fp_sam = sam_wf[sam_wf$asthma == 0,]
lf_fp_sam = sam_lf[sam_lf$asthma == 0,]
lf_fp_sam$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$asthma == 0,]
lf_fp_serum = serum_lf[serum_lf$asthma == 0,]
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"])
########################################################################
rm(npa_lf, npa_wf, sam_lf, sam_wf, serum_lf, serum_wf)

58
plot_data_ns.R Normal file
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#!/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_mediators.R")
#===============================
# data assignment for plots
#================================
#-----------
# npa
#-----------
wf_fp_npa = npa_wf[npa_wf$T1_resp_score != 3,]
lf_fp_npa = npa_lf[npa_lf$T1_resp_score != 3,]
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$mediator)
#-----------
# sam
#-----------
wf_fp_sam = sam_wf[sam_wf$T1_resp_score != 3,]
lf_fp_sam = sam_lf[sam_lf$T1_resp_score != 3,]
lf_fp_sam$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$T1_resp_score != 3,]
lf_fp_serum = serum_lf[serum_lf$T1_resp_score != 3,]
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"])
########################################################################
rm(npa_lf, npa_wf, sam_lf, sam_wf, serum_lf, serum_wf, fp_adults_ics)