We load the packages we will use:
We create a database:
# Creation of dataset
set.seed(2)
df <- data.frame(del=rexp(100)*5,
event=sample(c(0, 1, 2),100,replace=TRUE,prob = c(0.3, 0.6, 0.1)),
group=sample(c("A", "B"),100,replace=TRUE))
df$event_surv <- ifelse(df$event==0, 0, 1)| del | event | group | event_surv |
|---|---|---|---|
| 9.3267622 | 0 | A | 0 |
| 2.0237404 | 1 | A | 1 |
| 0.7332633 | 2 | B | 1 |
| 8.6535486 | 1 | B | 1 |
| 0.4476309 | 1 | A | 1 |
| 3.3344882 | 2 | B | 1 |
| 5.3718343 | 1 | B | 1 |
| 7.5581465 | 1 | A | 1 |
We create the differents survfit objects we will use :
# if one group
fit <- cuminc(df$del, df$event)
fit_surv <- survfit(Surv(del, event_surv)~1, data=df)
# if more than one group
fit_gp <- cuminc(df$del, df$event, df$group)
fit_surv_gp <- survfit(Surv(del, event_surv)~group, data=df)ggcompetingrisks1 functionThis function plots cumulative incidence curves. For
cuminc objects it’s a ggplot2 version of
plot.cuminc.
Arguments
ggcompetingrisks1(
fit, an object of a
class cmprsk::cuminc - created with
cmprsk::cuminc function.
Warning, the event
variable must be without spaces.
gnames, a vector with
group names. If not supplied then will be extracted from
fit object (cuminc only).
gsep, a separator that extracts group names and event names
from gnames object (cuminc only).
multiple_panels, if TRUE then groups will be
plotted in different panels (cuminc only).
event_suppr value of events that you don’t want to plot
lwd line thickness
palette the color
palette to be used.
Default is palette from hue_pal
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.
labs_event character
vector specifying legend labels for the events if more than one. Used to
replace the names of the events from the fit. Should be given in the
same order as those events
type_group if there is more
than one group, used to specify if you want to differentiate the groups
by different colors (“color”), different line types (“linetype”) or both
(“color_linetype”).
Default is "color"
type_event if there is more than one event, used to specify
if you want to differentiate the events by different colors (“color”),
different line types (“linetype”) or both (“color_linetype”).
Default is "linetype".
If more than
one group and more than one event, “color” will be used for
type_group and “linetype” will be used for
type_event.
alpha see
conf.int, scaling actor for the ribbon. The default value
is 0.05.
conf.int if TRUE then additional
layer (geom_ribbon) is added around the point estimate.
The ribon is plotted with boundries +-
qnorm(1-alpha/2)*standard deviation.
Standard
deviation is estimated with cif.ci method.
Default is
FALSE
conf.int.alpha numeric value
specifying confidence fill color transparency. Value should be in [0,
1], where 0 is full transparency and 1 is no transparency.
legend character specifying legend position. Allowed values
are one of c(“top”, “bottom”, “left”, “right”, “none”).
Default is “top” side position. to remove the legend use legend =
“none”.
Legend position can be also specified using a
numeric vector c(x, y).
In this case it is possible to
position the legend inside the plotting area. x and y are the
coordinates of the legend box.
Their values should be
between 0 and 1. c(0,0) corresponds to the “bottom left” and c(1,1)
corresponds to the “top right” position. For instance use legend =
c(0.8, 0.2).
legend.title legend title.
ggtheme function, ggplot2 theme name. Default
value is . Allowed values include ggplot2 official themes: see
\link[ggplot2]{theme}}. <br>…further arguments passed to the function}
for customizing the plot.
)
ggcombine functionThis function combine ggsurvplot and ggcompeting risks in a same plot.
Arguments
ggcombine(
list_obj, list of objects of a
class ggsurvplot or ggcompetingrisks1.
name_obj, a
vector with plot names.
linetype_obj, a vector with
plot groups (to differenciate groups by linetype, only for cumulative
incidence).
)
fill_survival_data functionThis function return a data frame with survival data, used to color the space between two survival curves
Arguments
fill_survival_data(
fit, a survfit object
)
ggrisktable functionArguments
ggrisktable(
fit, an object of class
survfit
data, a dataset used to fit survival curves
risk.table.type, risk table type. Allowed values :
c(“absolute”, “percentage”, “abs_pct”, “nrisk_cumcensor”,
“nrisk_cumevents”)
survtable, a character string
specifying the type of survival table to plot
title,
the title of the plot
risk.table.title, the title to
be used for the risk table
break.time.by, numeric
value controlling time axis breaks. Default value is NULL.
palette, the color palette to be used
color, if “group” : whole line of number at risk in color
y.text, logical. Default is TRUE. If FALSE, show bars
instead of names in text annotations
y.text.col,
logical. Default value is FALSE. If TRUE, the table labels will be
colored according to the strata. You can also specify the colors. Only
the label or the bar will be colored.
fontsize, text
font size
tables.theme, function, ggplot2 theme name
(see ggplot2 page)
color,
color to be used for the survival curves
legend,
legend position. Allowed values are one of c(“top”, “bottom”, “left”,
“right”, “none”). If “none” no legend at the top of the risk table.
...
)
This document is a work of the statistics team in the Biostatistics and Medical Information Department at Saint-Louis Hospital in Paris (SBIM).
Developed and updated by Noémie Bigot and Anouk Walter-Petrich
noemie.bigot@aphp.fr; anouk.walter-petrich@u-paris.fr
Based on The R Graph Gallery by Yan Holtz.