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checked and tidy up scripts for plots for non-severe

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Tanushree Tunstall 2020-12-07 16:51:16 +00:00
parent f2b778ace7
commit dde2cc9494
3 changed files with 63 additions and 64 deletions
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44
non_severe/check_stats.R
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@ -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$T1_resp_score)
table(fp_adults$obesity)
table(fp_adults_ics$T1_resp_score)
table(fp_adults_ics$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)