From 3338de800a9d73d4ddd9fe57f60ec2e242fe6b65 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Mon, 7 Dec 2020 16:55:17 +0000
Subject: [PATCH] added and moved plot_data for non-asthmatics and non-severe
 analysis

---
 plot_data_na.R | 59 ++++++++++++++++++++++++++++++++++++++++++++++++++
 plot_data_ns.R | 58 +++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 117 insertions(+)
 create mode 100755 plot_data_na.R
 create mode 100644 plot_data_ns.R

diff --git a/plot_data_na.R b/plot_data_na.R
new file mode 100755
index 0000000..10baa13
--- /dev/null
+++ b/plot_data_na.R
@@ -0,0 +1,59 @@
+#!/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)
diff --git a/plot_data_ns.R b/plot_data_ns.R
new file mode 100644
index 0000000..e7b2eab
--- /dev/null
+++ b/plot_data_ns.R
@@ -0,0 +1,58 @@
+#!/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)