R/heatmap_VICI.R

In vici: Vaccine Induced Cellular Immunogenicity with Bivariate Modeling

#'A heatmap function for displaying
#'
#'Internal function for displaying significance heatmap when multiple conditions are tested
#'
#'@param res_2plot a \code{data.frame}
#'
#'@param inter a logical flag indicating whether we are in the interarm setting or not.
#'Default is \code{TRUE}.
#'
#'@return a \code{ggplot2} plot object
#'
#'@author Boris Hejblum
#'
#'@keywords internal
#'
#'@import ggplot2

heatmap_vici <- function(res_2plot, inter=TRUE, baseline=NULL){
  
  if(inter){
    p <- ggplot(data = res_2plot) +
      geom_tile(aes_string(x="Stimulation", y="response", fill="pvalue"), color="white") +
      theme_minimal() +
      theme(panel.grid = element_blank()) +
      ggtitle("Arm effect on ICS response",
              subtitle = "taking into account background response levels") +
      labs(caption = "made with VICI") +
      ylab("ICS response") +
      scale_fill_manual(values = c("red4", "red2", "coral2", "grey70", "grey75", "grey80", "grey85","grey90", "grey95"),
                        breaks = c("[0,0.001)", "[0.001,0.01)", "[0.01,0.05)", "[0.05,0.1)", "[0.1,0.2)", "[0.2,0.3)", "[0.3,0.4)", "[0.4,0.5)", "[0.5,1)"),
                        labels = c("[0,0.001[", "[0.001,0.01[", "[0.01,0.05[", "[0.05,0.1[", "[0.1,0.2[", "[0.2,0.3[", "[0.3,0.4[", "[0.4,0.5[", "[0.5,1]"),
                        name="P-value",
                        limits = c("[0,0.001)", "[0.001,0.01)", "[0.01,0.05)", "[0.05,0.1)", "[0.1,0.2)", "[0.2,0.3)", "[0.3,0.4)", "[0.4,0.5)", "[0.5,1)")
      ) + facet_wrap(c("Arm"), labeller = "label_both")
  }else{
    p <- ggplot(data = res_2plot) +
      geom_tile(aes_string(x="Stimulation", y="response", fill="pvalue"), color="white") +
      theme_minimal() +
      theme(panel.grid = element_blank()) +
      ggtitle(paste0("Intra-arm vaccine effect on ICS responses compared to baseline ", baseline),
              subtitle = "taking into account background response levels") +
      labs(caption = "made with VICI") +
      ylab("ICS response") +
      scale_fill_manual(values = c("red4", "red2", "coral2", "grey70", "grey75", "grey80", "grey85","grey90", "grey95"),
                        breaks = c("[0,0.001)", "[0.001,0.01)", "[0.01,0.05)", "[0.05,0.1)", "[0.1,0.2)", "[0.2,0.3)", "[0.3,0.4)", "[0.4,0.5)", "[0.5,1)"),
                        labels = c("[0,0.001[", "[0.001,0.01[", "[0.01,0.05[", "[0.05,0.1[", "[0.1,0.2[", "[0.2,0.3[", "[0.3,0.4[", "[0.4,0.5[", "[0.5,1]"),
                        name="P-value",
                        limits = c("[0,0.001)", "[0.001,0.01)", "[0.01,0.05)", "[0.05,0.1)", "[0.1,0.2)", "[0.2,0.3)", "[0.3,0.4)", "[0.4,0.5)", "[0.5,1)")
      ) + facet_wrap(c("Timepoint"), labeller = "label_both")
  }

  return(p)
}