CODEWITHSUNDEEP
rstatisticssurvival-analysis
Ellen Heidinger
Ellen Heidinger

Reputation: 13

R Survival curve with two groups looks weird

I have estimated a Kaplan-Meier with two group using this code:

test3 <- survfit(Surv(wave, con3) ~ sex, data = consult3)
ggsurvplot(test3, color = "#2E9FDF",
       risk.table = TRUE, risk.table.y.text.col = TRUE)

and even though it produces a KM, it looks very weird and does not show me 2 different survival curves for sex==1 or sex==2. Does anybody know what I might have done wrong? Thanks!!

1

Upvotes: 1

Views: 289

Answers (1)

Allan Cameron
Allan Cameron

Reputation: 173793

It's always better to include some sample data so we can see where the problem lies. However, let's see if we can create some data that will replicate your problem:

library(survival)
library(survminer)

set.seed(69)

consult3 <- data.frame(sex = rep(1:2, each = 50),
                       con3 = c(rbinom(50, 1, 0.2), rbinom(50, 1, 0.4)),
                       wave = sample(3, 100, TRUE))

Now, using your code, we can get a similar-looking result:

test3 <- survfit(Surv(wave, con3) ~ sex, data = consult3)

ggsurvplot(test3, risk.table = TRUE, color = "#2E9FDF",
           risk.table.y.text.col = TRUE)

As far as I can tell, the problem with this is that you have set a single colour aesthetic. The solution is to just remove this:

ggsurvplot(test3, risk.table = TRUE, risk.table.y.text.col = TRUE)

If you want control over the colour of the lines, use palette instead of color:

ggsurvplot(test3, palette = c("red", "forestgreen"), alpha = 0.5,
           risk.table = TRUE, risk.table.y.text.col = TRUE)

enter image description here Created on 2020-09-19 by the reprex package (v0.3.0)

Upvotes: 1

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