checked and tidy up scripts for plots for non-severe

non_asthmatics/plot_data_na.R

@@ -1,60 +0,0 @@
-#!/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"])
-########################################################################
-

non_severe/check_stats.R

@@ -12,21 +12,23 @@ source("Header_TT.R")
 # Input
 #=============
 source("data_extraction_mediators.R")
-source("read_data.R")
+#source("read_data.R")
 
 ########################################################################
 #=============
 # Data extraction for non-severe
 #=============
-table(fp_adults$T1_resp_score)
+table(fp_adults_ics$T1_resp_score)
-table(fp_adults$obesity)
+table(fp_adults_ics$obesity)
 
-df = fp_adults[fp_adults$T1_resp_score<3,]
+df = fp_adults_ics[fp_adults_ics$T1_resp_score<3,]
 table(df$obesity)
 
 df_ob = df[df$obesity == 1,]
 df_nob = df[df$obesity == 0,]
 
+rm(npa_lf, npa_wf, sam_lf, sam_wf, serum_lf, serum_wf, fp_adults_ics)
+
 #============
 # npa
 #============
@@ -38,6 +40,8 @@ foo = data.frame(df$obesity, df$vl_pfu_ul_npa2)
 na_c = sum(is.na(foo$df.vl_pfu_ul_npa2))
 nrow(df) - na_c
 
+tapply(df$vl_pfu_ul_npa2, df$obesity, median, na.rm = T)
+tapply(df$vl_pfu_ul_npa2, df$obesity, summary, na.rm = T)
 
 # 1l29: t1
 wilcox.test(df_ob$il29_npa1, df_nob$il29_npa1)
@@ -46,6 +50,8 @@ foo = data.frame(df$obesity, df$il29_npa1)
 na_c = sum(is.na(foo$df.il29_npa1))
 nrow(df) - na_c
 
+tapply(df$il29_npa1, df$obesity, median, na.rm = T)
+tapply(df$il29_npa1, df$obesity, summary, na.rm = T)
 
 # tnfr1: t3
 wilcox.test(df_ob$tnfr1_npa3, df_nob$tnfr1_npa3)
@@ -55,6 +61,11 @@ na_c = sum(is.na(foo$df.tnfr1_npa3))
 nrow(df) - na_c
 
 
+tapply(df$tnfr1_npa3, df$obesity, median, na.rm = T)
+tapply(df$tnfr1_npa3, df$obesity, summary, na.rm = T)
+
+boxplot(df_ob$tnfr1_npa3, df_nob$tnfr1_npa3)
+
 # rantes: t1
 wilcox.test(df_ob$rantes_npa1, df_nob$rantes_npa1)
 
@@ -73,6 +84,9 @@ foo = data.frame(df$obesity, df$tarc_sam3)
 na_c = sum(is.na(foo$df.tarc_sam3))
 nrow(df) - na_c
 
+tapply(df$tarc_sam3, df$obesity, median, na.rm = T)
+
+
 # il13: t3
 wilcox.test(df_ob$il13_sam3
             , df_nob$il13_sam3)
@@ -81,6 +95,9 @@ foo = data.frame(df$obesity, df$il13_sam3)
 na_c = sum(is.na(foo$df.il13_sam3))
 nrow(df) - na_c
 
+tapply(df$il13_sam3, df$obesity, median, na.rm = T)
+
+
 # eotaxin: t1
 wilcox.test(df_ob$eotaxin_sam1
             , df_nob$eotaxin_sam1)
@@ -89,6 +106,8 @@ foo = data.frame(df$obesity, df$eotaxin_sam1)
 na_c = sum(is.na(foo$df.eotaxin_sam1))
 nrow(df) - na_c
 
+tapply(df$eotaxin_sam1, df$obesity, median, na.rm = T)
+
 
 #============
 # serum
@@ -101,6 +120,9 @@ foo = data.frame(df$obesity, df$ifna2a_serum1)
 na_c = sum(is.na(foo$df.ifna2a_serum1))
 nrow(df) - na_c
 
+tapply(df$ifna2a_serum1, df$obesity, median, na.rm = T)
+
+
 # mip17: t1
 wilcox.test(df_ob$mip17_serum1, 
             df_nob$mip17_serum1)
@@ -109,6 +131,8 @@ foo = data.frame(df$obesity, df$mip17_serum1)
 na_c = sum(is.na(foo$df.mip17_serum1))
 nrow(df) - na_c
 
+tapply(df$mip17_serum1, df$obesity, median, na.rm = T)
+
 # il1: t1
 wilcox.test(df_ob$il1_serum1
             , df_nob$il1_serum1)
@@ -117,6 +141,11 @@ foo = data.frame(df$obesity, df$il1_serum1)
 na_c = sum(is.na(foo$df.il1_serum1))
 nrow(df) - na_c
 
+tapply(df$il1_serum1, df$obesity, median, na.rm = T)
+tapply(df$il1_serum1, df$obesity, summary, na.rm = T)
+boxplot(df_ob$il1_serum1, df_nob$il1_serum1)
+
+
 # ifna2a: t2 
 wilcox.test(df_ob$ifna2a_serum2, 
             df_nob$ifna2a_serum2)
@@ -125,6 +154,9 @@ foo = data.frame(df$obesity, df$ifna2a_serum2)
 na_c = sum(is.na(foo$df.ifna2a_serum2))
 nrow(df) - na_c
 
+
+tapply(df$ifna2a_serum2, df$obesity, median, na.rm = T)
+
 # ifna2a: t3
 wilcox.test(df_ob$ifna2a_serum3, 
             df_nob$ifna2a_serum3)
@@ -133,6 +165,9 @@ foo = data.frame(df$obesity, df$ifna2a_serum3)
 na_c = sum(is.na(foo$df.ifna2a_serum3))
 nrow(df) - na_c
 
+tapply(df$ifna2a_serum3, df$obesity, median, na.rm = T)
+
+
 # ifnb: t3
 wilcox.test(df_ob$ifnb_serum3
             , df_nob$ifnb_serum3)
@@ -141,3 +176,4 @@ foo = data.frame(df$obesity, df$ifnb_serum3)
 na_c = sum(is.na(foo$df.ifnb_serum3))
 nrow(df) - na_c
 
+tapply(df$ifnb_serum3, df$obesity, median, na.rm = T)

stats_check.R

@@ -12,6 +12,12 @@ wf_npa = wf_fp_npa
 wf_sam = wf_fp_sam
 wf_serum = wf_fp_serum
 ############################################################
+# Numbers
+table(fp_adults_ics$asthma, fp_adults_ics$obesity)
+
+table(fp_adults_ics$obesity)
+
+
 #=========
 # t1
 #=========
@@ -24,6 +30,23 @@ length(wf_npa$il12p70_npa1) - sum(is.na(wf_npa$il12p70_npa1))
 tapply(wf_npa$eotaxin3_npa1, wf_npa$obesity, mean, na.rm = T)
 tapply(wf_npa$eotaxin3_npa1, wf_npa$obesity, median, na.rm = T)
 
+
+npa_wf_a = npa_wf[npa_wf$asthma == 1,] 
+npa_wf_na = npa_wf[npa_wf$asthma == 0,]
+
+wilcox.test(npa_wf_a$il4_npa1[npa_wf_a$obesity == 1]
+            , npa_wf_a$il4_npa1[npa_wf_a$obesity == 0], paired = F)
+
+length(npa_wf_a$il4_npa1) - sum(is.na(npa_wf_a$il4_npa1))
+
+wilcox.test(npa_wf_a$il13_npa1[npa_wf_a$obesity == 1]
+            , npa_wf_a$il13_npa1[npa_wf_a$obesity == 0], paired = F)
+
+wilcox.test(npa_wf_na$il4_npa1[npa_wf_na$obesity == 1]
+            , npa_wf_na$il4_npa1[npa_wf_na$obesity == 0], paired = F)
+wilcox.test(npa_wf_na$il13_npa1[npa_wf_na$obesity == 1]
+            , npa_wf_na$il13_npa1[npa_wf_na$obesity == 0], paired = F)
+
 #=========
 # t2
 #=========