From dde2cc9494d91fd032526d473f3c70f95c4fc6ed Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Mon, 7 Dec 2020 16:51:16 +0000 Subject: [PATCH] checked and tidy up scripts for plots for non-severe --- non_asthmatics/plot_data_na.R | 60 ----------------------------------- non_severe/check_stats.R | 44 ++++++++++++++++++++++--- stats_check.R | 23 ++++++++++++++ 3 files changed, 63 insertions(+), 64 deletions(-) delete mode 100755 non_asthmatics/plot_data_na.R diff --git a/non_asthmatics/plot_data_na.R b/non_asthmatics/plot_data_na.R deleted file mode 100755 index 34640a9..0000000 --- a/non_asthmatics/plot_data_na.R +++ /dev/null @@ -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$mediator == "vitd"]) -######################################################################## - diff --git a/non_severe/check_stats.R b/non_severe/check_stats.R index fa75589..06bc88e 100755 --- a/non_severe/check_stats.R +++ b/non_severe/check_stats.R @@ -12,21 +12,23 @@ source("Header_TT.R") # Input #============= source("data_extraction_mediators.R") -source("read_data.R") +#source("read_data.R") ######################################################################## #============= # Data extraction for non-severe #============= -table(fp_adults$T1_resp_score) -table(fp_adults$obesity) +table(fp_adults_ics$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) diff --git a/stats_check.R b/stats_check.R index e2bb218..7d01038 100755 --- a/stats_check.R +++ b/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 #=========