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dded paired unpaired stats scripts

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Tanushree Tunstall 2020-10-23 11:32:51 +01:00
parent b0c06b9704
commit 7add917155
4 changed files with 333 additions and 7 deletions
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#!/usr/bin/Rscript
getwd()
setwd('~/git/covid_analysis/')
getwd()
############################################################
# TASK: basic plots
# useful links:
# http://www.sthda.com/english/wiki/ggplot2-dot-plot-quick-start-guide-r-software-and-data-visualization
############################################################
# source data
source("read_data.R")
############################################################
#=========================
# output: paired_analysis
#=========================
stats_time_paired = paste0(outdir_stats, "stats_paired_v3.csv")
############################################################
# data assignment for stats
wf = wf_data
lf = lf_data
########################################################################
# Pairwise stats by timepoint: wilcoxon paired analysis with correction
########################################################################
# with adjustment: fdr and BH are identical
my_adjust_method = "BH"
stats_by_timepoint = compare_means(value~timepoint, group.by = "mediator"
, data = lf
, paired = TRUE
, p.adjust.method = my_adjust_method)
# check: satisfied!!!!
wilcox.test(wf$sESelectin_ngmL_t1, wf$sESelectin_ngmL_t2, paired = T)
wilcox.test(wf$sRAGE_pgmL_t1, wf$sRAGE_pgmL_t2, paired = T)
# delete unnecessary column
stats_by_timepoint = subset(stats_by_timepoint, select = -c(.y.))
# reflect stats method correctly
stats_by_timepoint$method
stats_by_timepoint$method = gsub("Wilcoxon", "Wilcoxon_paired", stats_by_timepoint$method)
stats_by_timepoint$method
# replace "." in colnames with "_"
colnames(stats_by_timepoint)
#names(stats_by_timepoint) = gsub("\.", "_", names(stats_by_timepoint)) # weird!!!!
colnames(stats_by_timepoint) = c("mediator"
,"group1"
,"group2"
,"p"
,"p_adj"
,"p_format"
,"p_signif"
,"method" )
colnames(stats_by_timepoint)
# add an extra column for padjust_signif
stats_by_timepoint$padjust_signif = round(stats_by_timepoint$p_adj, digits = 2)
# add appropriate symbols for padjust_signif
#stats_by_timepoint = stats_by_timepoint %>%
# mutate(padjust_signif = case_when(padjust_signif == 0.05 ~ "."
# , padjust_signif <0.05 ~ '*'
# , padjust_signif <=0.01 ~ '**'
# , padjust_signif <=0.001 ~ '***'
# , padjust_signif <=0.0001 ~ '****'
# , TRUE ~ 'ns'))
stats_by_timepoint = dplyr::mutate(stats_by_timepoint, padjust_signif = case_when(padjust_signif == 0.05 ~ "."
, padjust_signif <=0.0001 ~ '****'
, padjust_signif <=0.001 ~ '***'
, padjust_signif <=0.01 ~ '**'
, padjust_signif <0.05 ~ '*'
, TRUE ~ 'ns'))
# reorder columns
print("preparing to reorder columns...")
colnames(stats_by_timepoint)
my_col_order2 = c("mediator"
, "group1"
, "group2"
, "method"
, "p"
, "p_format"
, "p_signif"
, "p_adj"
, "padjust_signif")
if( length(my_col_order2) == ncol(stats_by_timepoint) && isin(my_col_order2, colnames(stats_by_timepoint)) ){
print("PASS: Reordering columns...")
stats_by_timepoint_f = stats_by_timepoint[, my_col_order2]
print("Successful: column reordering")
print("formatted df called:'stats_by_timepoint_f'")
cat('\nformatted df has the following dimensions\n')
print(dim(stats_by_timepoint_f ))
} else{
cat(paste0("FAIL:Cannot reorder columns, length mismatch"
, "\nExpected column order for: ", ncol(stats_by_timepoint)
, "\nGot:", length(my_col_order2)))
quit()
}
#******************
# write output file
#******************
cat("Paired stats by timepoint will be:", stats_time_paired)
write.csv(stats_by_timepoint_f, stats_time_paired, row.names = FALSE)