In ellessenne/KMunicate-package: KMunicate-Style Kaplan–Meier Plots

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The {KMunicate} package can be used to produce Kaplan-Meier plots in the style recommended following the KMunicate study by TP Morris et al. (2019).

In this vignette, we'll see learn how to produce such a plot using the {KMunicate} package.

Data

We will be using the brcancer dataset, which comes bundled with {KMunicate}:

data("brcancer", package = "KMunicate")
str(brcancer)

Single-Arm Plot

We start by creating a KMunicate-style plot for all study subjects. First, we load the package:

library(KMunicate)

Then, we fit a Kaplan-Meier curve using the survfit function from the {survival} package:

fit <- survfit(Surv(rectime, censrec) ~ 1, data = brcancer)
fit

Then, we need to define the horizontal axis of the plot. For instance, we can define 5 equally-spaced breaks between time zero and the largest observed time:

ts <- seq(0, max(brcancer$rectime), length.out = 5)
ts

Finally, we can pass fit and ts to the KMunicate() function to simply obtain a plot:

KMunicate(fit = fit, time_scale = ts)

Multiple-Arms Plot

A multiple-arms plot will be automatically produced if the survfit object has covariates in it. For instance, if we fit the Kaplan-Meier estimator by treatment arm:

fit2 <- survfit(Surv(rectime, censrec) ~ hormon, data = brcancer)
fit2

We will be using the same time scale as before (ts), and the call to KMunicate() is analogous:

KMunicate(fit = fit2, time_scale = ts)

Customisation

The KMunicate() function contains a few options to customise the produced plot. First, we can pass a ggplot2 theme to the .theme argument:

KMunicate(fit = fit2, time_scale = ts, .theme = ggplot2::theme_minimal())

We can also pass custom colour (and fill) scales:

KMunicate(
  fit = fit2,
  time_scale = ts,
  .color_scale = ggplot2::scale_color_brewer(type = "qual", palette = "Set2"),
  .fill_scale = ggplot2::scale_fill_brewer(type = "qual", palette = "Set2")
)

We can customise the transparency of the point-wise confidence intervals via the .alpha argument:

KMunicate(fit = fit2, time_scale = ts, .alpha = 0.1)

We can customise the label of the horizontal axis:

KMunicate(fit = fit2, time_scale = ts, .xlab = "New Label (Time in Days, Actually)")

We can customise the relative size of risk tables and plots, although the default should generally work fine for most scenarios:

KMunicate(fit = fit2, time_scale = ts, .rel_heights = c(1, 1, 1))

Custom Fonts

Assuming you have set up your computer and R session to support custom fonts (e.g. using a ragg graphics device), you can produce plots with custom fonts via the .ff argument of the KMunicate() function. Examples of using ragg can be found here.

A Better Plot

We can combine all the above to obtain an (arguably) much better plot:

KMunicate(
  fit = fit2,
  time_scale = ts,
  .theme = ggplot2::theme_minimal(),
  .xlab = "Time (in days)",
  .color_scale = ggplot2::scale_color_brewer(type = "qual", palette = "Set2"),
  .fill_scale = ggplot2::scale_fill_brewer(type = "qual", palette = "Set2")
)

Further Customisation Options

As of version 0.2.0, {KMunicate} provide additional arguments to customise the final plot.

You can customise the size of each Kaplan-Meier curve via the .size argument:

KMunicate(
  fit = fit2,
  time_scale = ts,
  .size = 2
)

You can customise the linetype scale via the .linetype_scale argument:

KMunicate(
  fit = fit2,
  time_scale = ts,
  .linetype_scale = ggplot2::scale_linetype_manual(values = c("dotted", "dashed"))
)

You can customise the location of the legend via the .legend_position argument, or you can even suppress it fully:

KMunicate(
  fit = fit2,
  time_scale = ts,
  .reverse = TRUE,
  .legend_position = c(0, 1)
)

KMunicate(
  fit = fit2,
  time_scale = ts,
  .reverse = TRUE,
  .legend_position = "none"
)

You can add custom annotations via the .annotate argument:

KMunicate(
  fit = fit2,
  time_scale = ts,
  .annotate = ggplot2::annotate(geom = "text", x = 365, y = 0.5, label = "Some annotation")
)

You can add customise labels and title with the .xlab, .ylab, and .title arguments:

KMunicate(
  fit = fit2,
  time_scale = ts,
  .xlab = "New Label, X Axis",
  .ylab = "New Label, Y Axis",
  .title = "New Title Who Dis"
)

ellessenne/KMunicate-package documentation built on May 19, 2024, 6:03 a.m.