simplePheWAS:

#' @export
# Outputs a nicely formatted summary of results.

summarization_paragraph <- function(phenotypes, genotypes, results){
  sig <- filter(results,bonferroni&!is.na(p))
  phe_with_desc <- addPhecodeInfo(sig$phenotype)
  sig <- inner_join(sig, phe_with_desc, by=c("phenotype"="phecode"))
  pw_codes <- sig$phenotype
  for (c in pw_codes){
    result_row <- sig[sig$phenotype==c,]
    cat("\n")
    cat("PheWAS code ",c," represents ",result_row$description,". ",sep='')
    # % won't be the same for each code - doesn't count NAs
    cat(result_row$n_cases," patients in the dataset, or ",
        round(result_row$n_cases*100/result_row$n_total,2),"% of all patients, have ",
        result_row$description,". ",sep='')
    cat("The allelic odds ratio between SNP ",result_row$snp," and ",
        result_row$description," is ",result_row$OR,
        ", meaning that a patient with the ",result_row$snp," allele is roughly ",
        result_row$OR," times as likely to have ",result_row$description,
        " as a patient without it. ",sep='')
    tmp <- phenotypes[!is.na(phenotypes[,c]),]
    res <- left_join(tmp[,c("id",c)],genotypes,by="id")
    ctable <- table(res[,2:3])
    cat("Of people presenting with ",result_row$description,", ",
        round(100*ctable["TRUE","0"]/sum(ctable["TRUE",]),2),"% have genotype 0, ",
        round(100*ctable["TRUE","1"]/sum(ctable["TRUE",]),2),"% have genotype 1, and ",
        round(100*ctable["TRUE","2"]/sum(ctable["TRUE",]),2),"% have genotype 2. ",sep='')
    cat("Of people presenting without ",result_row$description,", ",
        round(100*ctable["FALSE","0"]/sum(ctable["FALSE",]),2),"% have genotype 0, ",
        round(100*ctable["FALSE","1"]/sum(ctable["FALSE",]),2),"% have genotype 1, and ",
        round(100*ctable["FALSE","2"]/sum(ctable["FALSE",]),2),"% have genotype 2. ",sep='')
    cat("Of the ",sum(ctable[,"0"])," people with genotype 0, ",
        round(100*ctable["TRUE","0"]/sum(ctable[,"0"]),2),"% have ",
        result_row$description,", ",sep='')
    cat("of the ",sum(ctable[,"1"])," people with genotype 1, ",
        round(100*ctable["TRUE","1"]/sum(ctable[,"1"]),2),"% have ",
        result_row$description,", ",sep='')
    cat("and of the ",sum(ctable[,"2"])," people with genotype 2, ",
        round(100*ctable["TRUE","2"]/sum(ctable[,"2"]),2),"% have ",
        result_row$description,".\n",sep='')
    cat("\n")
  }
}

summarization_list <- function(phenotypes, genotypes, results){
  sig <- filter(results,bonferroni&!is.na(p))
  phe_with_desc <- addPhecodeInfo(sig$phenotype)
  sig <- inner_join(sig, phe_with_desc, by=c("phenotype"="phecode"))
  pw_codes <- sig$phenotype
  for (c in pw_codes){
    result_row <- sig[sig$phenotype==c,]
    cat("\n")
    cat("For PheWAS code ",c," (",result_row$description,"):\n",sep='')
    # % won't be the same for each code - doesn't count NAs
    cat("--> Patients in dataset with phenotype: ",result_row$n_cases," (",
        round(result_row$n_cases*100/result_row$n_total,2),"% of total)\n",sep='')
    cat("--> Odds ratio with SNP ",result_row$snp,": ",result_row$OR,"\n",sep='')
    tmp <- phenotypes[!is.na(phenotypes[,c]),]
    res <- left_join(tmp[,c("id",c)],genotypes,by="id")
    ctable <- table(res[,2:3])
    cat("--> Of people presenting with ",result_row$description,": ",
        round(100*ctable["TRUE","0"]/sum(ctable["TRUE",]),2),"% have genotype 0, ",
        round(100*ctable["TRUE","1"]/sum(ctable["TRUE",]),2),"% have genotype 1, and ",
        round(100*ctable["TRUE","2"]/sum(ctable["TRUE",]),2),"% have genotype 2","\n",sep='')
    cat("--> Of people presenting without ",result_row$description,": ",
        round(100*ctable["FALSE","0"]/sum(ctable["FALSE",]),2),"% have genotype 0, ",
        round(100*ctable["FALSE","1"]/sum(ctable["FALSE",]),2),"% have genotype 1, and ",
        round(100*ctable["FALSE","2"]/sum(ctable["FALSE",]),2),"% have genotype 2","\n",sep='')
    cat("--> Of the ",sum(ctable[,"0"])," people with genotype 0: ",
        round(100*ctable["TRUE","0"]/sum(ctable[,"0"]),2),"% have ",
        result_row$description,"\n",sep='')
    cat("--> Of the ",sum(ctable[,"1"])," people with genotype 1: ",
        round(100*ctable["TRUE","1"]/sum(ctable[,"1"]),2),"% have ",
        result_row$description,"\n",sep='')
    cat("--> Of the ",sum(ctable[,"2"])," people with genotype 2: ",
        round(100*ctable["TRUE","2"]/sum(ctable[,"2"]),2),"% have ",
        result_row$description,"\n",sep='')
    cat("\n")
  }
}

summarization_table <- function(phenotypes, genotypes, results){
  sig <- filter(results,bonferroni&!is.na(p))
  phe_with_desc <- addPhecodeInfo(sig$phenotype)
  sig <- inner_join(sig, phe_with_desc, by=c("phenotype"="phecode"))
  pw_codes <- sig$phenotype
  for (c in pw_codes){
    result_row <- sig[sig$phenotype==c,]
    tmp <- phenotypes[!is.na(phenotypes[,c]),]
    res <- left_join(tmp[,c("id",c)],genotypes,by="id")
    colnames(res)[2] <- result_row$description
    ctable <- table(res[,2:3])
    cat("\n")
    print(ctable)
    cat("--> Odds Ratio: ",result_row$OR,"; p=",result_row$p,sep='')
    cat("\n\n")
  }
}

summarization_all <- function(phenotypes,genotypes,results){
  sig <- filter(results,bonferroni&!is.na(p))
  phe_with_desc <- addPhecodeInfo(sig$phenotype)
  sig <- inner_join(sig, phe_with_desc, by=c("phenotype"="phecode"))
  pw_codes <- sig$phenotype
  for (c in pw_codes){
    result_row <- sig[sig$phenotype==c,]
    cat("For PheWAS code ",c," (",result_row$description,"):\n",sep='')
    # % won't be the same for each code - doesn't count NAs
    cat("--> Patients in dataset with phenotype: ",result_row$n_cases," (",
        round(result_row$n_cases*100/result_row$n_total,2),"% of total)\n",sep='')
    cat("--> Odds ratio with SNP ",result_row$snp,": ",result_row$OR,"\n",sep='')
    tmp <- phenotypes[!is.na(phenotypes[,c]),]
    res <- left_join(tmp[,c("id",c)],genotypes,by="id")
    ctable <- table(res[,2:3])
    cat("--> Of people presenting with ",result_row$description,": ",
        round(100*ctable["TRUE","0"]/sum(ctable["TRUE",]),2),"% have genotype 0, ",
        round(100*ctable["TRUE","1"]/sum(ctable["TRUE",]),2),"% have genotype 1, and ",
        round(100*ctable["TRUE","2"]/sum(ctable["TRUE",]),2),"% have genotype 2","\n",sep='')
    cat("--> Of people presenting without ",result_row$description,": ",
        round(100*ctable["FALSE","0"]/sum(ctable["FALSE",]),2),"% have genotype 0, ",
        round(100*ctable["FALSE","1"]/sum(ctable["FALSE",]),2),"% have genotype 1, and ",
        round(100*ctable["FALSE","2"]/sum(ctable["FALSE",]),2),"% have genotype 2","\n",sep='')
    cat("--> Of the ",sum(ctable[,"0"])," people with genotype 0: ",
        round(100*ctable["TRUE","0"]/sum(ctable[,"0"]),2),"% have ",
        result_row$description,"\n",sep='')
    cat("--> Of the ",sum(ctable[,"1"])," people with genotype 1: ",
        round(100*ctable["TRUE","1"]/sum(ctable[,"1"]),2),"% have ",
        result_row$description,"\n",sep='')
    cat("--> Of the ",sum(ctable[,"2"])," people with genotype 2: ",
        round(100*ctable["TRUE","2"]/sum(ctable[,"2"]),2),"% have ",
        result_row$description,"\n",sep='')
    cat("\n")
  }
  print(phewas_manhattan(results))
}