added all_output_plots.R, legend_adjustment.R and stats_corr.R

stats_corr.R

@@ -0,0 +1,89 @@
+#!/usr/bin/Rscript   
+getwd()
+setwd('~/git/covid_analysis/')
+getwd()
+############################################################
+# TASK: Pairwise correaltion and P-values: T1
+############################################################
+# source data
+source("read_data.R")
+
+# clear unwanted variables
+rm(my_data)
+############################################################
+#=============
+# Output
+#=============
+# corr analysis
+my_spearman_corr = paste0(outdir_stats, "corr_spearman_t1_v3.csv")
+my_pvals = paste0(outdir_stats, "corr_pvalues_t1_v3.csv")
+############################################################
+# data assignment for stats
+wf = wf_data
+lf = lf_data
+########################################################################
+#           Pairwise correaltions and analyses
+########################################################################
+
+head(wf$outcomes)
+wf <- wf[order(wf$outcomes),]
+
+# subset t1 data
+wf_t1 = cbind(wf[c(1:3)],  wf %>% dplyr:: select(grep("_t1", names(wf))))
+colnames(wf_t1)
+
+# assign nice column names
+my_colnames = c("id"
+                , "studygroup"
+                , "outcomes"
+                #, "idcol"
+                , "Angiopoietin2"
+                , "PF"       
+                , "PSelectin"     
+                , "sESelectin"  
+                , "sICAM1"
+                , "sRAGE"     
+                , "sVCAM1")
+
+if (length(my_colnames) == length(my_colnames)){
+  print("PASS: Reassigning column names...")
+  colnames(wf_t1) = my_colnames 
+} else{
+  cat(paste0("FAIL:Cannot assign column names, length mismatch"
+             , "\nExpected length: ", length(orig_colanmes)
+             , "\nGot:", length(my_colnames)))
+  quit()
+}    
+
+print('formatted colnames are:'); print(colnames(wf_t1))
+
+# inspect
+class(wf_t1); str(wf_t1)
+
+# Compute a matrix of correlation p-values
+start_med = which(colnames(wf_t1) == "Angiopoietin2")
+end_med = which(colnames(wf_t1) == "sVCAM1")
+
+#---------------
+# Data for corr analysis
+#---------------
+corr_M = wf_t1[start_med:end_med]
+
+my_corr1 = cor(corr_M
+              , method = "spearman"
+              , use =  "pairwise.complete.obs")
+
+my_corr = psych::corr.test(corr_M
+                           , method = "spearman"
+                           , use =  "pairwise.complete.obs")$r
+
+my_pval =  psych::corr.test(corr_M
+                            , method = "spearman"
+                            , adjust = "none"
+                            , use =  "pairwise.complete.obs")$p
+
+#******************
+# write output file: correlations and pvalues
+#******************
+write.csv(my_corr, my_spearman_corr, row.names = TRUE)
+write.csv(my_pval, my_pvals, row.names = TRUE)