R/boxplot_VICI.R

In vici: Vaccine Induced Cellular Immunogenicity with Bivariate Modeling

#'Plotting function for displaying boxplots and associated p-values
#'
#'Internal function for displaying significance boxplots
#'
#'@param res_2plot a \code{data.frame}.
#'@param pval_2plot a \code{data.frame} with the p-values to display.
#'@param inter a logical flag indicating whether we are in the interarm setting or not.
#'Default is \code{TRUE}.
#'@param baseline baseline value used in title when \code{inter} is \code{FALSE}.
#'Default is \code{NULL}.
#'
#'@return a \code{ggpubr} plot object
#'
#'@author Boris Hejblum
#'
#'@keywords internal
#'
#'@import ggplot2
#'@import ggpubr
#'@import RColorBrewer

boxplot_VICI <- function(data_df, pval_2plot, response_name, input, inter=TRUE, baseline=NULL){
  
  
  p <- NULL
  if(inter){
    data_df$arm <- relevel(data_df$arm, ref=input$selectRefArmInter)
    suppressWarnings(
      if(input$jiter == "None"){
        p <- ggboxplot(na.omit(data_df), x="stim", y="response", color= "arm", palette = "RdGy",
                       alpha=0.3,)+
          theme_classic() +
          theme(panel.grid.major.x = element_blank()) +
          scale_color_brewer(palette = input$color) +
          stat_pvalue_manual(data = pval_2plot, label = "pvalue_format",
                             tip.length = 0.025) +
          ylab(paste0("Response ", response_name)) +
          xlab("Stimulation") +
          ggtitle(paste0("Arm effect on ", response_name),
                  subtitle = "p-values taking into account background response levels through bivariate modeling") +
          labs(caption = "made with VICI")
      }else{
      p <- ggboxplot(na.omit(data_df), x="stim", y="response", color= "arm", palette = "RdGy",
                  alpha=0.3,
                  add="jitter",
                  shape = as.numeric(input$jiter))+
        theme_classic() +
        theme(panel.grid.major.x = element_blank()) +
        scale_color_brewer(palette = input$color) +
        stat_pvalue_manual(data = pval_2plot, label = "pvalue_format",
                           tip.length = 0.025) +
        ylab(paste0("Response ", response_name)) +
        xlab("Stimulation") +
        ggtitle(paste0("Arm effect on ", response_name),
                subtitle = "p-values taking into account background response levels through bivariate modeling") +
        labs(caption = "made with VICI")
      },
    )
  }else{
    data_df$time <- relevel(data_df$time, ref=input$selectRefTimeIntra)
    if(input$jiter == "None"){
      p <- ggboxplot(na.omit(data_df), x="stim", y="response", color= "time", palette = "RdGy",
                     alpha=0.3,) + 
        theme_classic() +
        theme(panel.grid.major.x = element_blank()) +
        scale_color_brewer(palette = input$color)+
        stat_pvalue_manual(data = pval_2plot, label = "pvalue_format",
                           tip.length =  0.025) +
        ylab(paste0("Response ", response_name)) +
        xlab("Stimulation") +
        ggtitle(paste0("Intra-arm vaccine effect on ", response_name, " compared to baseline ", baseline),
                subtitle = "p-values taking into account background response levels through bivariate modeling") +
        labs(caption = "made with VICI")
    }else{
      p <- ggboxplot(na.omit(data_df), x="stim", y="response", color= "time", palette = "RdGy",
                     alpha=0.3,
                     add="jitter",
                     shape = as.numeric(input$jiter))+
        theme_classic() +
        theme(panel.grid.major.x = element_blank()) +
        scale_color_brewer(palette = input$color)+
        stat_pvalue_manual(data = pval_2plot, label = "pvalue_format",
                           tip.length =  0.025) +
        ylab(paste0("Response ", response_name)) +
        xlab("Stimulation") +
        ggtitle(paste0("Intra-arm vaccine effect on ", response_name, " compared to baseline ", baseline),
                subtitle = "p-values taking into account background response levels through bivariate modeling") +
        labs(caption = "made with VICI")
    }
  }
  return(p)

}