R/helper_functions.R

In aneuraz/multiWAS: multiWAS

#' make_manhattan
#' @export
make_manhattan <- function(res, p.type, plot.type, plot_height) {
  dev.new()
  plot_height
  res <- res %>% 
    dplyr::filter_(paste0(p.type, "<=", 0.05)) %>%
    manhattan_plot(result = ., type = plot.type)
  
  g <- plotly::ggplotly(res ,tooltip = c('label', 'text'), height = plot_height)
  dev.off()
  g
}

#' make_dumbbell
#' @export
make_dumbbell <- function(res, plot_height, db_type) {
  if(nrow(res) > 0) {
    res <- dumbbell_plot(res, db_type =db_type)
    plotly::ggplotly(res, tooltip = c('CODE_LABEL_TIP', 'CI95'), height = plot_height)
  }
  
}

#'make_print_table
#'@export
make_print_table <- function(res, cols_to_remove, boot) {
  
  if(nrow(res) > 0) {
    
    result_to_print <- res %>%
      dplyr::filter(p_fdr <= 0.05)
    
    if(nrow(result_to_print) > 0) {
      result_to_print <- result_to_print %>%
        arrange(p.value) %>%
        mutate(cases = paste0(cases,'/',cases+cases0, ' (',round(cases/(cases+cases0),2),')'),
               control = paste0(control,'/',control+control0, ' (',round(control/(control+control0),2),')'),
               OR = paste0(round(OR,1),' [',round(CI_inf,1),'-',round(CI_sup,1),']'),
               p.value = format(p.value, digits = 2, scientific = TRUE),
               p_fdr = format(p_fdr, digits = 2, scientific = TRUE),
               p_bonf = format(p_bonf, digits = 2, scientific = TRUE)) %>%
        select_( .dots = cols_to_remove) #-CODE, -CI_inf, -CI_sup, -cases0,-control0)
      
      if (boot) {
        result_to_print <- result_to_print %>%
          mutate(OR_bootstrap = paste0('[',format(CI_OR_inf, digits = 2, scientific = TRUE),'-',format(CI_OR_sup, digits = 2, scientific = TRUE),']'),
                 pvalue_bootstrap = paste0('[',format(p_inf, digits = 2, scientific = TRUE),'-',format(p_sup, digits = 2, scientific = TRUE),']')) %>%
          select(-term, -CI_OR_inf, -CI_OR_sup, -p_inf,-p_sup)
      }
      
    } else {
      result_to_print <- data.frame(Results = 'No result reached the FDR correction threshold.')
    }
    
    # if (boot) {
    #   result_to_print <- result_to_print %>%
    #     mutate(OR_bootstrap = paste0('[',format(CI_OR_inf, digits = 2, scientific = TRUE),'-',format(CI_OR_sup, digits = 2, scientific = TRUE),']'),
    #            pvalue_bootstrap = paste0('[',format(p_inf, digits = 2, scientific = TRUE),'-',format(p_sup, digits = 2, scientific = TRUE),']')) %>%
    #     select(-term, -CI_OR_inf, -CI_OR_sup, -p_inf,-p_sup)
    # } else{
    #   result_to_print
    # }
    
  } else {
    result_to_print<- data.frame(Results = 'No result.')
  }
  return(result_to_print)
}