R/plotpower.R

In PDXpower: Time to Event Outcome in Experimental Designs of Pre-Clinical Studies

##' @title A function to generate a four-panel power curve under specified
##' number of PDX lines and number of individuals per PDX lines per treatment
##' @param object object of class 'PowerTable'.
##' @param ylim limit of y axis.
##' @param x.axis.n.breaks number of breaks of the x axis. Default is 10.
##' @param y.axis.n.breaks number of breaks of the y axis. Default is 10.
##' @param cut.off a number to indicate the cut-off for power analysis. Default is 0.8.
##' @param legend.position the position of legends ("none", "left", "right", "bottom", "top", or two-element numeric vector).
##' @return a figure generated by ggplot.
##' @export
##'

plotpower <- function(object, ylim = c(0, 0.1), x.axis.n.breaks = 10, y.axis.n.breaks = 10,
                      cut.off = 0.8, legend.position = "right") {

  if (!inherits(object, "PowerTable"))
    stop("Use only with 'PowerTable' objects.\n")

  print <- object$print
  fixed.effect <- object$fixed.effect

  if (object$beta == 0) {
    ylab <- "Type I error"
  } else {
    ylab <- "Power"
  }

  if (fixed.effect) {
    if (print == "both") {
      object <- data.frame(object$NofLine, object$NofAnimals,
                           object$ANOVAfix,
                           object$Coxfix)

      colnames(object) <- c("PDOX lines", "Number of Animals", "ANOVAfix", "Coxfix")

      object$`Number of Animals` <- as.factor(object$`Number of Animals`)

      a1 <- ggplot2::ggplot(object, aes(x = `PDOX lines`, y = ANOVAfix,
                                                 group = `Number of Animals`)) +
        ggplot2::geom_line(aes(linetype = `Number of Animals`)) +
        ggplot2::geom_point(colour="white", stroke = 5) +
        ggplot2::geom_text(aes(label = `Number of Animals`)) +
        ggplot2::theme_bw() +
        ggplot2::theme(legend.position = legend.position,
                       panel.border = element_blank(),
                       panel.grid.major = element_blank(),
                       panel.grid.minor = element_blank(),
                       axis.line = element_line(colour = "black")) +
        ggplot2::scale_x_continuous(n.breaks = x.axis.n.breaks) +
        ggplot2::scale_y_continuous(limits = ylim,
                                    expand = c(0, 0),
                                    n.breaks = y.axis.n.breaks) +
        ggplot2::geom_hline(yintercept = cut.off) +
        ggplot2::ylab(paste(ylab, "for ANOVA fixed effects")) +
        ggplot2::xlab("Number of PDX lines")

      a2 <- ggplot2::ggplot(object, aes(x = `PDOX lines`, y = Coxfix,
                                         group = `Number of Animals`)) +
        ggplot2::geom_line(aes(linetype = `Number of Animals`)) +
        ggplot2::geom_point(colour="white", stroke = 5) +
        ggplot2::geom_text(aes(label = `Number of Animals`)) +
        ggplot2::theme_bw() +
        ggplot2::theme(legend.position = legend.position,
                       panel.border = element_blank(),
                       panel.grid.major = element_blank(),
                       panel.grid.minor = element_blank(),
                       axis.line = element_line(colour = "black")) +
        ggplot2::scale_x_continuous(n.breaks = x.axis.n.breaks) +
        ggplot2::scale_y_continuous(limits = ylim,
                                    expand = c(0, 0),
                                    n.breaks = y.axis.n.breaks) +
        ggplot2::geom_hline(yintercept = cut.off) +
        ggplot2::ylab(paste(ylab, "for Cox fixed effects")) +
        ggplot2::xlab("Number of PDX lines")

      ggpubr::ggarrange(a1, a2, ncol = 2, nrow = 1, common.legend = TRUE,
                        legend = "right")


    } else if (print == "ANOVA") {

      object <- data.frame(object$NofLine, object$NofAnimals, object$ANOVAfix)

      colnames(object) <- c("PDOX lines", "Number of Animals", "ANOVAfix")

      object$`Number of Animals` <- as.factor(object$`Number of Animals`)

      ggplot2::ggplot(object, aes(x = `PDOX lines`, y = ANOVAfix,
                                                 group = `Number of Animals`)) +
        ggplot2::geom_line(aes(linetype = `Number of Animals`)) +
        ggplot2::geom_point(colour="white", stroke = 5) +
        ggplot2::geom_text(aes(label = `Number of Animals`)) +
        ggplot2::theme_bw() +
        ggplot2::theme(legend.position = legend.position,
                       panel.border = element_blank(),
                       panel.grid.major = element_blank(),
                       panel.grid.minor = element_blank(),
                       axis.line = element_line(colour = "black")) +
        ggplot2::scale_x_continuous(n.breaks = x.axis.n.breaks) +
        ggplot2::scale_y_continuous(limits = ylim,
                                    expand = c(0, 0),
                                    n.breaks = y.axis.n.breaks) +
        ggplot2::geom_hline(yintercept = cut.off) +
        ggplot2::ylab(paste(ylab, "for ANOVA fixed effects")) +
        ggplot2::xlab("Number of PDX lines")

    } else {

      object <- data.frame(object$NofLine, object$NofAnimals, object$Coxfix)

      colnames(object) <- c("PDOX lines", "Number of Animals", "Coxfix")

      object$`Number of Animals` <- as.factor(object$`Number of Animals`)

      ggplot2::ggplot(object, aes(x = `PDOX lines`, y = Coxfix,
                                         group = `Number of Animals`,
                                         color = `Number of Animals`)) +
        ggplot2::geom_line(aes(linetype = `Number of Animals`)) +
        ggplot2::geom_point(colour="white", stroke = 5) +
        ggplot2::geom_text(aes(label = `Number of Animals`)) +
        ggplot2::theme_bw() +
        ggplot2::theme(legend.position = legend.position,
                       panel.border = element_blank(),
                       panel.grid.major = element_blank(),
                       panel.grid.minor = element_blank(),
                       axis.line = element_line(colour = "black")) +
        ggplot2::scale_x_continuous(n.breaks = x.axis.n.breaks) +
        ggplot2::scale_y_continuous(limits = ylim,
                                    expand = c(0, 0),
                                    n.breaks = y.axis.n.breaks) +
        ggplot2::geom_hline(yintercept = cut.off) +
        ggplot2::ylab(paste(ylab, "for Cox fixed effects")) +
        ggplot2::xlab("Number of PDX lines")

    }
  } else {
    if (print == "both") {
      object <- data.frame(object$NofLine, object$NofAnimals,
                           object$ANOVArandom,
                           object$Coxrandom)

      colnames(object) <- c("PDOX lines", "Number of Animals", "ANOVArandom", "Coxrandom")

      object$`Number of Animals` <- as.factor(object$`Number of Animals`)

      a1 <- ggplot2::ggplot(object,
                            aes(x = `PDOX lines`, y = ANOVArandom,
                                         group = `Number of Animals`)) +
        ggplot2::geom_line(aes(linetype = `Number of Animals`)) +
        ggplot2::geom_point(colour="white", stroke = 5) +
        ggplot2::geom_text(aes(label = `Number of Animals`)) +
        ggplot2::theme_bw() +
        ggplot2::theme(legend.position = legend.position,
                       panel.border = element_blank(),
                       panel.grid.major = element_blank(),
                       panel.grid.minor = element_blank(),
                       axis.line = element_line(colour = "black")) +
        ggplot2::scale_x_continuous(n.breaks = x.axis.n.breaks) +
        ggplot2::scale_y_continuous(limits = ylim,
                                    expand = c(0, 0),
                                    n.breaks = y.axis.n.breaks) +
        ggplot2::geom_hline(yintercept = cut.off) +
        ggplot2::ylab(paste(ylab, "for mixed effects ANOVA model")) +
        ggplot2::xlab("Number of PDX lines")

      a2 <- ggplot2::ggplot(object,
                            aes(x = `PDOX lines`, y = Coxrandom,
                                         group = `Number of Animals`)) +
        ggplot2::geom_line(aes(linetype = `Number of Animals`)) +
        ggplot2::geom_point(colour="white", stroke = 5) +
        ggplot2::geom_text(aes(label = `Number of Animals`)) +
        ggplot2::theme_bw() +
        ggplot2::theme(legend.position = legend.position,
                       panel.border = element_blank(),
                       panel.grid.major = element_blank(),
                       panel.grid.minor = element_blank(),
                       axis.line = element_line(colour = "black")) +
        ggplot2::scale_x_continuous(n.breaks = x.axis.n.breaks) +
        ggplot2::scale_y_continuous(limits = ylim,
                                    expand = c(0, 0),
                                    n.breaks = y.axis.n.breaks) +
        ggplot2::geom_hline(yintercept = cut.off) +
        ggplot2::ylab(paste(ylab, "for Cox's frailty model")) +
        ggplot2::xlab("Number of PDX lines")

      ggpubr::ggarrange(a1, a2, ncol = 2, nrow = 1, common.legend = TRUE,
                        legend = "right")

    } else if (print == "ANOVA") {

      object <- data.frame(object$NofLine, object$NofAnimals,
                           object$ANOVArandom)

      colnames(object) <- c("PDOX lines", "Number of Animals", "ANOVArandom")

      object$`Number of Animals` <- as.factor(object$`Number of Animals`)

      ggplot2::ggplot(object, aes(x = `PDOX lines`, y = ANOVArandom,
                                           group = `Number of Animals`)) +
        ggplot2::geom_line(aes(linetype = `Number of Animals`)) +
        ggplot2::geom_point(colour="white", stroke = 5) +
        ggplot2::geom_text(aes(label = `Number of Animals`)) +
        ggplot2::theme_bw() +
        ggplot2::theme(legend.position = legend.position,
                       panel.border = element_blank(),
                       panel.grid.major = element_blank(),
                       panel.grid.minor = element_blank(),
                       axis.line = element_line(colour = "black")) +
        ggplot2::scale_x_continuous(n.breaks = x.axis.n.breaks) +
        ggplot2::scale_y_continuous(limits = ylim,
                                    expand = c(0, 0),
                                    n.breaks = y.axis.n.breaks) +
        ggplot2::geom_hline(yintercept = cut.off) +
        ggplot2::ylab(paste(ylab, "for mixed effects ANOVA model")) +
        ggplot2::xlab("Number of PDX lines")
    } else {

      object <- data.frame(object$NofLine, object$NofAnimals,
                           object$Coxrandom)

      colnames(object) <- c("PDOX lines", "Number of Animals", "Coxrandom")

      object$`Number of Animals` <- as.factor(object$`Number of Animals`)

      ggplot2::ggplot(object,
                      aes(x = `PDOX lines`, y = Coxrandom,
                                   group = `Number of Animals`)) +
        ggplot2::geom_line(aes(linetype = `Number of Animals`)) +
        ggplot2::geom_point(colour="white", stroke = 5) +
        ggplot2::geom_text(aes(label = `Number of Animals`)) +
        ggplot2::theme_bw() +
        ggplot2::theme(legend.position = legend.position,
                       panel.border = element_blank(),
                       panel.grid.major = element_blank(),
                       panel.grid.minor = element_blank(),
                       axis.line = element_line(colour = "black")) +
        ggplot2::scale_x_continuous(n.breaks = x.axis.n.breaks) +
        ggplot2::scale_y_continuous(limits = ylim,
                                    expand = c(0, 0),
                                    n.breaks = y.axis.n.breaks) +
        ggplot2::geom_hline(yintercept = cut.off) +
        ggplot2::ylab(paste(ylab, "for Cox's frailty model")) +
        ggplot2::xlab("Number of PDX lines")
    }

  }

}