15/5/2020 Survival plots have never been so informative

Survival plots have never been so

informative
Marcin Kosinski

Motivation
Example
Comparisons
base package
survMisc package

This vigne e covers changes between versions 0.1.0 and 0.2.0.

Motivation

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15/5/2020 Survival plots have never been so informative

Hadley Wickham’s ggplot2 version 2.0 revolution (h p://www.r-bloggers.com/ggplot-2-0-0/), at the

end of 2015, triggered many crashes in dependent R packages, that finally led to deletions of few
packages from The Comprehensive R Archive Network (h ps://cran.r-project.org/). It occured that
survMisc package was removed from CRAN on 27th of January 2016 and R world remained
helpless in the struggle with the elegant visualizations of survival analysis. Then a new tool -
survminer (h ps://cran.r-project.org/package=survminer) package, created by Alboukadel
Kassambara (h ps://github.com/kassambara) - appeared on the R survival scene to fill the gap in
visualizing the Kaplan-Meier estimates of survival curves in elegant grammar of graphics like way.
This blog presents main features of core ggsurvplot() function from survminer package, which
creates the most informative, elegant and flexible survival plots that I have seen!
During the development of RTCGA (h p://rtcga.github.io/RTCGA/) package (about which I wrote
here (h p://r-addict.com/2016/05/04/RTCGA-Quick-Guide.html)) we
(h ps://github.com/orgs/RTCGA/people) encountered a need to provide the simplest possible
interface to estimates of survival curves for biotechnologists and the discovery of ggsurvplot()
(h p://www.sthda.com/english/wiki/survminer-r-package-survival-data-analysis-and-
visualization) was a bull’s-eye! Many have tried (h ps://github.com/hadley/ggplot2/issues/1080) to
provide a package or function for ggplot2-like plots that would present the basic tool of survival
analysis: Kaplan-Meier estimates of survival curves, but none of earlier a empts have provided
such a rich structure of features and flexibility as survminer. On basis of estimates of survival
curves one can infere on differences in survival times between compared groups, so survival plots
are very useful and can be seen in almost every publication in the field of survival analysis and time
to event models.

Example
After regular installation

install.packages('survminer')
source("https://bioconductor.org/biocLite.R")
biocLite("RTCGA.clinical") # data for examples

we can create simple estimates of survival curves just after we put survfit (survival package)
object into ggsurvplot() function. Let’s have a look at differences in survival times between
patients suffering from Ovarian Cancer (Ovarian serous cystadenocarcinoma) and patients
suffering from Breast Cancer (Breast invasive carcinoma), where data were collected by The Cancer
Genome Atlas Project (h p://cancergenome.nih.gov/).

library(survminer)
library(RTCGA.clinical)
survivalTCGA(BRCA.clinical, OV.clinical,
extract.cols = "admin.disease_code") -> BRCAOV.survInfo
library(survival)
fit <- survfit(Surv(times, patient.vital_status) ~ admin.disease_code,
data = BRCAOV.survInfo)
# Visualize with survminer
ggsurvplot(fit, data = BRCAOV.survInfo, risk.table = TRUE)

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15/5/2020 Survival plots have never been so informative

This simple plot presents, in an elegant way, estimates of survival probability depending on days
from cancer diagnostics grouped by cancer types and an informative risk set table, which shows the
number of patients that were under observation in the specific period of time. Survival analysis is a
specific field of data analysis because of the censored time to event data, so risk set size is a must in
visual inference.
After few improvements (#1 (h ps://github.com/kassambara/survminer/issues/1), #2
(h ps://github.com/kassambara/survminer/issues/2), #3
(h ps://github.com/kassambara/survminer/issues/3), #4
(h ps://github.com/kassambara/survminer/issues/4), #7
(h ps://github.com/kassambara/survminer/issues/7), #8
(h ps://github.com/kassambara/survminer/issues/8), #12
(h ps://github.com/kassambara/survminer/issues/12), #28
(h ps://github.com/kassambara/survminer/issues/28)), made by Alboukadel in version 0.2.0, one
can create a powerful, informative survival plot with such specification of parameters

ggsurvplot(
fit, # survfit object with calculated statistics.
data = BRCAOV.survInfo, # data used to fit survival curves.
risk.table = TRUE, # show risk table.
pval = TRUE, # show p-value of log-rank test.
conf.int = TRUE, # show confidence intervals for
# point estimaes of survival curves.
xlim = c(0,2000), # present narrower X axis, but not affect
# survival estimates.
break.time.by = 500, # break X axis in time intervals by 500.
ggtheme = theme_minimal(), # customize plot and risk table with a theme.
risk.table.y.text.col = T, # colour risk table text annotations.
risk.table.y.text = FALSE # show bars instead of names in text annotations
# in legend of risk table
)

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15/5/2020 Survival plots have never been so informative

Each parameter is described in the correspoding comment, but I would like to emphasize the xlim
parameter which controls limits of the X axis but does not affect the survival curves, that are taking
into account all possible times. Another brilliant parameter is break.time.by that affects survival
plots and the risk set table - this would not be so easy to create it by yourself. Also a ggtheme
parameter is beneficial for simple plot customization. Finally, risk.table.y.text and
risk.table.y.text.col (for which I have provided a user requests) are useful parameters that
change text (often too long and redundand) from risk table legend into narrow, coloured bar. This
saves a lot of space in the final plot.

Comparisons
Even though survMisc (h ps://cran.r-project.org/package=survMisc) have returned on CRAN, I’ve
appreciated survminer so much that I would not look anymore for other solutions. Check why: at
the end I present survival curves that can be obtained with the usage of base package and survMisc
package.

base package

plot(fit) # base

It looks pre y… base…

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15/5/2020 Survival plots have never been so informative

plot(fit, col=c("orange","purple"), lty=c(1:2), lwd=3, # base with some customization

conf.int = TRUE, xmax = 2000)
# add a legend
legend(100, .2, c("Ovarian Cancer", "Breast Cancer"),
lty = c(1:2), col=c("orange","purple"))

I haven’t seen examples with risk table and adding legend isn’t so quick as in survminer. Moreover,
there are no minor axis breaks lines.

survMisc package

# install.packages('survMisc')
library(survMisc)
survMisc:::autoplot.survfit(fit) # no customization

Why colours are not asigned to any group? Where is the legend? Why there is so much white space
to the right? (Those were questions for the version of survMisc where this was an issue.) Where is
OX axis?

survMisc:::autoplot.survfit( # with some hard customization

fit,
type = "fill",
pVal=TRUE
) -> fit.survMisc
fit.survMisc$table <- fit.survMisc$table +
theme_minimal() + # theme(legend.position = "top")
coord_cartesian(xlim = c(0,2000))
fit.survMisc$plot <- fit.survMisc$plot +
theme_minimal() +
coord_cartesian(xlim = c(0,2000))
survMisc:::print.tableAndPlot(fit.survMisc)

Where is risk table? Why I can’t pass break.by.time to have informative minor X axis breaks? Why
the plot gets narrower when the legend in risk table gets wider and why I can’t do anything to
workaround this?

Never mind -> install.packages('survminer')

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