ggforest in R x tick mark font size

Question

I am trying to change the font size of the x axis tick to larger size and bold, but its not working in ggforest using ggpar. see ate attached image where I have circled the portion I need to change. Is there another way to modify the figure using ggforest.

cox1 <- coxph(mySurv ~ flyname, data = mydata_df)

p <- ggforest(cox1, data = mydata_df, fontsize = 1.5, cpositions = c(0.02, 0.10, 0.42))

ggpar(p, font.tickslab = c(12, "bold"))

Answer 1

Here's how you could modify ggforest() to use any font size you want (why not? it's really just a fancy ggplot, right?). As far as I can tell, this is pretty much doing manually what ggpar() would be doing otherwise.

Or, for a formal solution, you could open an issue on the survminer github. See that someone recently posted an issue there about font type; it might be worth seeing what develops from that.

First, the result:

library("survival")
library("survminer")
model <- coxph( Surv(time, status) ~ sex + rx + adhere, data = colon )
a <- ggforest(model)
b <- ggforest3(model, font.x.size = 20)
ggarrange(a,b)

And here is how I defined ggforest3() with a font.x.size parameter:

ggforest3 <- function (model,
          data = NULL,
          main = "Hazard ratio",
          cpositions = c(0.02,0.22, 0.4),
          fontsize = 0.7,
          refLabel = "reference",
          noDigits = 2,
          font.x.size = 20)
{
  # dependencies
  require(broom)
  require(survival)
  require(grid)
  .get_data <- function(fit, data = NULL, complain = TRUE) {
    if(is.null(data)){
      if (complain)
        warning ("The `data` argument is not provided. Data will be extracted from model fit.")
      data <- eval(fit$call$data)
      if (is.null(data))
        stop("The `data` argument should be provided either to ggsurvfit or survfit.")
    }
    data
  } # end dependencies
  
  conf.high <- conf.low <- estimate <- NULL
  stopifnot(inherits(model, "coxph"))
  data <- .get_data(model, data = data)
  terms <- attr(model$terms, "dataClasses")[-1]
  coef <- as.data.frame(tidy(model, conf.int = TRUE))
  gmodel <- glance(model)
  allTerms <- lapply(seq_along(terms), function(i) {
    var <- names(terms)[i]
    if (terms[i] %in% c("factor", "character")) {
      adf <- as.data.frame(table(data[, var]))
      cbind(var = var, adf, pos = 1:nrow(adf))
    }
    else if (terms[i] == "numeric") {
      data.frame(
        var = var,
        Var1 = "",
        Freq = nrow(data),
        pos = 1
      )
    }
    else {
      vars = grep(paste0("^", var, "*."), coef$term, value = TRUE)
      data.frame(
        var = vars,
        Var1 = "",
        Freq = nrow(data),
        pos = seq_along(vars)
      )
    }
  })
  allTermsDF <- do.call(rbind, allTerms)
  colnames(allTermsDF) <- c("var", "level", "N", "pos")
  inds <- apply(allTermsDF[, 1:2], 1, paste0, collapse = "")
  rownames(coef) <- gsub(coef$term, pattern = "`", replacement = "")
  toShow <- cbind(allTermsDF, coef[inds,])[, c("var",
                                               "level",
                                               "N",
                                               "p.value",
                                               "estimate",
                                               "conf.low",
                                               "conf.high",
                                               "pos")]
  toShowExp <- toShow[, 5:7]
  toShowExp[is.na(toShowExp)] <- 0
  toShowExp <- format(exp(toShowExp), digits = noDigits)
  toShowExpClean <- data.frame(toShow, pvalue = signif(toShow[,
                                                              4], noDigits + 1), toShowExp)
  toShowExpClean$stars <- paste0(
    round(toShowExpClean$p.value,
          noDigits + 1),
    " ",
    ifelse(toShowExpClean$p.value <
             0.05, "*", ""),
    ifelse(toShowExpClean$p.value < 0.01,
           "*", ""),
    ifelse(toShowExpClean$p.value < 0.001, "*",
           "")
  )
  toShowExpClean$ci <- paste0("(", toShowExpClean[, "conf.low.1"],
                              " - ", toShowExpClean[, "conf.high.1"], ")")
  toShowExpClean$estimate.1[is.na(toShowExpClean$estimate)] = refLabel
  toShowExpClean$stars[which(toShowExpClean$p.value < 0.001)] = "<0.001 ***"
  toShowExpClean$stars[is.na(toShowExpClean$estimate)] = ""
  toShowExpClean$ci[is.na(toShowExpClean$estimate)] = ""
  toShowExpClean$estimate[is.na(toShowExpClean$estimate)] = 0
  toShowExpClean$var = as.character(toShowExpClean$var)
  toShowExpClean$var[duplicated(toShowExpClean$var)] = ""
  toShowExpClean$N <- paste0("(N=", toShowExpClean$N, ")")
  toShowExpClean <- toShowExpClean[nrow(toShowExpClean):1,]
  rangeb <-
    range(toShowExpClean$conf.low, toShowExpClean$conf.high,
          na.rm = TRUE)
  breaks <- axisTicks(rangeb / 2, log = TRUE, nint = 7)
  rangeplot <- rangeb
  rangeplot[1] <- rangeplot[1] - diff(rangeb)
  rangeplot[2] <- rangeplot[2] + 0.15 * diff(rangeb)
  width <- diff(rangeplot)
  y_variable <- rangeplot[1] + cpositions[1] * width
  y_nlevel <- rangeplot[1] + cpositions[2] * width
  y_cistring <- rangeplot[1] + cpositions[3] * width
  y_stars <- rangeb[2]
  x_annotate <- seq_len(nrow(toShowExpClean))
  annot_size_mm <-
    fontsize * as.numeric(convertX(unit(theme_get()$text$size,
                                        "pt"), "mm"))
  p <- ggplot(toShowExpClean, aes(seq_along(var), exp(estimate))) +
    geom_rect(
      aes(
        xmin = seq_along(var) - 0.5,
        xmax = seq_along(var) +
          0.5,
        ymin = exp(rangeplot[1]),
        ymax = exp(rangeplot[2]),
        fill = ordered(seq_along(var) %% 2 + 1)
      )
    ) + scale_fill_manual(values = c("#FFFFFF33",
                                     "#00000033"),
                          guide = "none") + geom_point(pch = 15,
                                                       size = 4) + geom_errorbar(aes(ymin = exp(conf.low),
                                                                                     ymax = exp(conf.high)), width = 0.15) + geom_hline(yintercept = 1,
                                                                                                                                        linetype = 3) + coord_flip(ylim = exp(rangeplot)) +
    ggtitle(main) + scale_y_log10(
      name = "",
      labels = sprintf("%g",
                       breaks),
      expand = c(0.02, 0.02),
      breaks = breaks
    ) +
    theme_light() + theme(
      panel.grid.minor.y = element_blank(),
      panel.grid.minor.x = element_blank(),
      panel.grid.major.y = element_blank(),
      legend.position = "none",
      panel.border = element_blank(),
      axis.title.y = element_blank(),
      axis.text.y = element_blank(),
      # Modified here
      axis.text.x = element_text(size=font.x.size),
      # End modification
      axis.ticks.y = element_blank(),
      plot.title = element_text(hjust = 0.5)
    ) +
    xlab("") + annotate(
      geom = "text",
      x = x_annotate,
      y = exp(y_variable),
      label = toShowExpClean$var,
      fontface = "bold",
      hjust = 0,
      size = annot_size_mm
    ) + annotate(
      geom = "text",
      x = x_annotate,
      y = exp(y_nlevel),
      hjust = 0,
      label = toShowExpClean$level,
      vjust = -0.1,
      size = annot_size_mm
    ) + annotate(
      geom = "text",
      x = x_annotate,
      y = exp(y_nlevel),
      label = toShowExpClean$N,
      fontface = "italic",
      hjust = 0,
      vjust = ifelse(toShowExpClean$level ==
                       "", 0.5, 1.1),
      size = annot_size_mm
    ) + annotate(
      geom = "text",
      x = x_annotate,
      y = exp(y_cistring),
      label = toShowExpClean$estimate.1,
      size = annot_size_mm,
      vjust = ifelse(toShowExpClean$estimate.1 ==
                       "reference", 0.5,-0.1)
    ) + annotate(
      geom = "text",
      x = x_annotate,
      y = exp(y_cistring),
      label = toShowExpClean$ci,
      size = annot_size_mm,
      vjust = 1.1,
      fontface = "italic"
    ) +
    annotate(
      geom = "text",
      x = x_annotate,
      y = exp(y_stars),
      label = toShowExpClean$stars,
      size = annot_size_mm,
      hjust = -0.2,
      fontface = "italic"
    ) + annotate(
      geom = "text",
      x = 0.5,
      y = exp(y_variable),
      label = paste0(
        "# Events: ",
        gmodel$nevent,
        "; Global p-value (Log-Rank): ",
        format.pval(gmodel$p.value.log, eps = ".001"),
        " \nAIC: ",
        round(gmodel$AIC, 2),
        "; Concordance Index: ",
        round(gmodel$concordance,
              2)
      ),
      size = annot_size_mm,
      hjust = 0,
      vjust = 1.2,
      fontface = "italic"
    )
  gt <- ggplot_gtable(ggplot_build(p))
  gt$layout$clip[gt$layout$name == "panel"] <- "off"
  ggpubr::as_ggplot(gt)
}