Survival Plots with Survminer - Blank Plot

Question

I'm currently having an issue with blank plots appearing in rmarkdown chunk outputs for survminer. Please see image below.

It makes output difficult as it includes a huge empty space while trying to author reports.

I've been investigating this issue and I've narrowed it down to having to do with this print 'newpage' argument -

My question is - can anybody explain what exactly is happening here? - why is there a 'blank' plot and how can I not have it show ? - what exactly is happening when I have newpage = F for the first plot and newpage = T for the second plot to not have the blank page show ? - is there any other method of NOT having the first blank plot show ?

Thank you!

EDIT:

Reproducible Example -

require(survminer)
require(survival)

Data <- data.frame(
X = sample(1:30),
Y = sample(c(1,0), 30, replace = TRUE),
Z = sample(c(1,0), 30, replace = TRUE)
)

ggsurvplot(
 survfit(Surv(Data$X, Data$Y) ~ Data$Z),
 risk.table = T,
 break.time.by = 12,
 risk.table.fontsize = 3,
 font.tickslab = 10,
 font.x = 11,
 xlab = 'Time (Months)',
 font.y = 11,
 font.main = 11,
 legend = c(0.8, .9),
 legend.title = '',
 risk.table.height = .20,
 risk.table.title = element_blank(),
 censor = F,
 pval = T,
 pval.coord = c(6, .00),
 pval.size = 4,
 surv.scale = 'percent',
 risk.table.y.text = F,
 palette = 'Set1'
)

Judo

Please show a MCVE : stackoverflow.com/help/how-to-ask, https://mcmap.net/q/40507/-how-to-make-a-great-r-reproducible-example How did you create plot_anylocaltreatment and plot_aggressive? – Basutoland

My apologies - I'm still fairly new. I've attached a reproducible example in the edit above. – Judo

Michael, try ditching the notebook and render as HTML. Addresses the issue for me. – Shirker

Answer 1

In order to print the survival plot with no leading blank plots, print just the plot object returned by ggsurvplot(). For example,

library(survival)
library(survminer)
fit <- survfit(Surv(time, status) ~ sex, data = lung)
p <- ggsurvplot(fit, data = lung)
print(p$plot)

Cistercian

This doesn't work if you have the table at the bottom. And if you do p$plot, you don't even need print() – Shirker

I guess what @Shirker means is the 'at risk table'. This is indeed not shown. You could also call p$table but then the 'at risk table' is nearly the same size as the plot. – Etherize

to also print the "at risk table" you can call p$table in a separate R chunk and resize it in the chunk options, e.g.: {r, fig.height = 4, fig.width = 5.5, position=center} p$plot and {r, fig.height = 1, fig.width = 5.5, position=center} p$table this way you will omit the blank page and can size plot and table separately. Dirty workaround though. – Bloomy

Answer 2

This seems to work for me :

plot.new() 
print(p,newpage = FALSE)

This will also work if the plot has the risk table. This solution is better than doing first plot(p$plot) and then plot(p$table) as suggested by others, because the table and plots remain nicely aligned.

Bilabial

Still works well in 2023. Thanks! – Fiesole