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Facet Survival Curves into Multiple Panels

Source: R/ggsurvplot_facet.R
ggsurvplot_facet.Rd

Draw multi-panel survival curves of a data set grouped by one or two variables.

Usage

ggsurvplot_facet(
  fit,
  data,
  facet.by,
  color = NULL,
  palette = NULL,
  legend.labs = NULL,
  pval = FALSE,
  pval.method = FALSE,
  pval.coord = NULL,
  pval.method.coord = NULL,
  nrow = NULL,
  ncol = NULL,
  scales = "fixed",
  short.panel.labs = FALSE,
  panel.labs = NULL,
  panel.labs.background = list(color = NULL, fill = NULL),
  panel.labs.font = list(face = NULL, color = NULL, size = NULL, angle = NULL),
  panel.labs.font.x = panel.labs.font,
  panel.labs.font.y = panel.labs.font,
  ...
)

Arguments

fit

an object of class survfit.

data

a dataset used to fit survival curves. If not supplied then data will be extracted from 'fit' object.

facet.by

character vector, of length 1 or 2, specifying grouping variables for faceting the plot. Should be in the data.

color

color to be used for the survival curves.

  • If the number of strata/group (n.strata) = 1, the expected value is the color name. For example color = "blue".

  • If n.strata > 1, the expected value is the grouping variable name. By default, survival curves are colored by strata using the argument color = "strata", but you can also color survival curves by any other grouping variables used to fit the survival curves. In this case, it's possible to specify a custom color palette by using the argument palette.

palette

the color palette to be used. Allowed values include "hue" for the default hue color scale; "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty". See details section for more information. Can be also a numeric vector of length(groups); in this case a basic color palette is created using the function palette.

legend.labs

character vector specifying legend labels. Used to replace the names of the strata from the fit. Should be given in the same order as those strata.

pval

logical value, a numeric or a string. If logical and TRUE, the p-value is added on the plot. If numeric, than the computet p-value is substituted with the one passed with this parameter. If character, then the customized string appears on the plot. See examples - Example 3.

pval.method

whether to add a text with the test name used for calculating the pvalue, that corresponds to survival curves' comparison - used only when pval=TRUE

pval.coord

numeric vector, of length 2, specifying the x and y coordinates of the p-value. Default values are NULL.

pval.method.coord

the same as pval.coord but for displaying log.rank.weights name

nrow, ncol

Number of rows and columns in the pannel. Used only when the data is faceted by one grouping variable.

scales

should axis scales of panels be fixed ("fixed", the default), free ("free"), or free in one dimension ("free_x", "free_y").

short.panel.labs

logical value. Default is FALSE. If TRUE, create short labels for panels by omitting variable names; in other words panels will be labelled only by variable grouping levels.

panel.labs

a list of one or two character vectors to modify facet label text. For example, panel.labs = list(sex = c("Male", "Female")) specifies the labels for the "sex" variable. For two grouping variables, you can use for example panel.labs = list(sex = c("Male", "Female"), rx = c("Obs", "Lev", "Lev2") ).

panel.labs.background

a list to customize the background of panel labels. Should contain the combination of the following elements:

  • color, linetype, size: background line color, type and size

  • fill: background fill color.

For example, panel.labs.background = list(color = "blue", fill = "pink").

panel.labs.font

a list of aestheics indicating the size (e.g.: 14), the face/style (e.g.: "plain", "bold", "italic", "bold.italic") and the color (e.g.: "red") and the orientation angle (e.g.: 45) of panel labels.

panel.labs.font.x, panel.labs.font.y

same as panel.labs.font but for x and y direction, respectively.

...

other arguments to pass to the function ggsurvplot.

Examples

library(survival)

# Facet by one grouping variables: rx
#::::::::::::::::::::::::::::::::::::::::::::::::::::::::
fit <- survfit( Surv(time, status) ~ sex, data = colon )
ggsurvplot_facet(fit, colon, facet.by = "rx",
                palette = "jco", pval = TRUE)


# Facet by two grouping variables: rx and adhere
#::::::::::::::::::::::::::::::::::::::::::::::::::::::::
ggsurvplot_facet(fit, colon, facet.by = c("rx", "adhere"),
                palette = "jco", pval = TRUE)



# Another fit
#::::::::::::::::::::::::::::::::::::::::::::::::::::::::
fit2 <- survfit( Surv(time, status) ~ sex + rx, data = colon )
ggsurvplot_facet(fit2, colon, facet.by = "adhere",
                palette = "jco", pval = TRUE)