R生存曲线图图例

Question

I have a table that looks like this:

ID Survival Event Allele
2   5   1   WildType
2   0   1   WildType
3   3   1   WildType
4   38  0   Variant

I want to do a kaplan meier plot, and tell me if wild type or variants tend to survive longer.

I have this code:

library(survival)
Table <-read.table("Table1",header=T)
fit=survfit(Surv(Table$Survival,Table$Event)~Table$Allele)
plot(fit,lty=2:3,col=3:4)

From the fit p value, I can see that the survival of these two groups have significantly different survival curves.

survdiff(formula = Surv(dat$Death, dat$Event) ~ dat$Allele, rho = 0)
#                            N Observed Expected (O-E)^2/E (O-E)^2/V 
#    dat$Allele=Variant   5592     3400     3503      3.00      8.63
#    dat$Allele=WildType  3232     2056     1953      5.39      8.63
#    Chisq= 8.6  on 1 degrees of freedom, p= 0.0033

The plot looks as expected (ie two curves).

All I want to do is put a legend on the plot, so that I can see which data is represented by the black and red lines, ie do the Wild Type or Variant survive longer.

I have tried these two commands:

lab <-gsub("x=","",names(fit$strata))
legend("top",legend=lab,col=3:4,lty=2:3,horiz=FALSE,bty='n')

The first command works (ie I get no error). The second command, I get this error:

Error in strwidth(legend, units = "user", cex = cex, font = text.font) : plot.new has not been called yet

I've tried reading forums etc., but none of the answers seem to work for me (for example, changing between top/topright/topleft etc. doesn't matter).

Edit 1: This is an example of a table for which I get this error:

    ID Survival Event Allele
25808   5   1   WTHomo
22196   0   1   Variant
22518   3   1   Variant
25013   38  0   Variant
27354   5   1   Variant
27223   4   1   Variant
22700   5   1   Variant
22390   24  1   Variant
17586   1   1   Variant

What exactly happens is: when I type the very last command ( legend("top",legend=lab,col=3:4,lty=2:3,horiz=FALSE,bty='n')), the XII window opens, except it's completely blank.

But then if you just type "plot(fit,lty=2:3,col=3:4)", the XII window and the plot appear.

Edit 2: Also, this graph will have two lines, how do I tell which line is which variable? Would the easiest way to do this be to type summary(fit) which gives me two tables. Then, whichever variable comes first in the table, I put in first in the legend?

Many thanks Eva

Answer 1

I too have had repeated problems with the "plot.new has not been called yet" error! Strangely, the error was intermittent and repeating the identical commands did not always result in the error! In my case, I found that by preceding the plotting command with

plot.new()

stopped the error from appearing! I have no idea why. Just as an aside, I also had no problem adding a legend to the survival plot using your command.

Answer 2

You can also do this using ggsurvplot() from survminer . Here is an example

library(survminer) # Contains ggsurvplot()
library(survival) # Contains survfit()
ggsurvplot(
  fit=survfit(Surv(time, censor) ~ Allele, data=your_data,type="kaplan-meier"), # Model
  xlab="Years",
  ylab="Overall survival probability",
  legend.labs=c("WildType","Variant"), # Assign names to groups which are shown in the plot
  conf.int = T, # Adds a 95%-confidence interval
  pval = T, # Displays the P-value in the plot
  pval.method = T # Shows the statistical method used for obtaining the P-value
)