Saving ggsurvplot() #152

kassambara · 2017-02-19T07:24:49Z

e-mail from a user

Hi Alboukadel,
How are you? I hope you’re doing good. I was trying to save a KM plot using survminer. However, when I try to save the figure with ggsave I got an error message as below. I did some online search but could not really find a solution. Could you please help?
Thanks in advance!
Serigne

require("survival")
require("survminer")
 
fit<- survfit(Surv(time, status) ~ sex, data = lung)
 
# Drawing survival curves
ggsurvplot(fit)
 
# Change font size, style and color
#++++++++++++++++++++++++++++++++++++
## Not run:
# Change font size, style and color at the same time
pp = ggsurvplot(fit, main = "Survival curve",
           font.main = c(16, "bold", "darkblue"),
           font.x = c(14, "bold.italic", "red"),
           font.y = c(14, "bold.italic", "darkred"),
           font.tickslab = c(12, "plain", "darkgreen"))
ggsave("C:\\serigne\\KMsurvival.jpeg", plot=pp)
Saving 6.1 x 7.27 in image
Error in UseMethod("grid.draw") :
  no applicable method for 'grid.draw' applied to an object of class "c('ggsurvplot', 'list')"

kassambara · 2017-02-19T07:26:25Z

ggsurvplot() returns a list of ggplots containing survival curves and optionally the risk table. You can’t directly save the list using ggsave(), but you can save the output of print(ggsurvplot).

First, please install the latest version of survminer:

if(!require(devtools)) install.packages("devtools")
devtools::install_github("kassambara/survminer", build_vignettes = FALSE)

Then, type this:

require("survival")
fit<- survfit(Surv(time, status) ~ sex, data = lung)

require("survminer")
survp <- ggsurvplot(fit, risk.table = TRUE)
ggsave(file = "ggsurv.pdf", print(survp))

It should work.

VincentGuyader · 2017-08-08T07:48:17Z

Hi,
How can I use ggsave if I dont need the "number at risk table" ?

require("survival")
fit<- survfit(Surv(time, status) ~ sex, data = lung)

require("survminer")
survp <- ggsurvplot(fit, risk.table = FALSE)
ggsave(file = "ggsurv.pdf", print(survp))

Saving 4.46 x 7 in image
Error in UseMethod("grid.draw") :
no applicable method for 'grid.draw' applied to an object of class "list"

kassambara · 2017-08-08T08:19:27Z

Hi,

To save ggsurvplot + risktable, use this:

pdf("survplot.pdf")
print(survp, newpage = FALSE)
dev.off()

To save only survival plots without the risk table, use this:

pdf("survplot.pdf")
print(survp$plot, newpage = FALSE)
dev.off()

or use this:

ggsave("survplot.pdf", surp$plot)

Phil-T · 2017-09-04T16:54:59Z

Im getting a similar error. Please see my code below.

fit<- survfit(Surv(time, dead) ~ copy_number, data = datain)
p <- ggsurvplot(fit, conf.int = TRUE, pval = TRUE,
main = "Survival",
palette = c("#ff0000", "#0000ff"),
font.main = c(10, "bold"),
font.x = c(8, "bold"),
font.y = c(8, "bold"),
font.tickslab = c(6, "bold"),
pval.size = 2,
size = 0.2,
censor.size = 1,
legend = "bottom"
)
p$plot <- p$plot + theme(legend.text = element_text(size = 4),
legend.title = element_text("", size = 4),
legend.key.size = unit(0.2, "cm"))

ggsave(filename= "/home/philserver/Desktop/mt_amp.tiff", print(p), device = "tiff", height = 2, width = 2, dpi = 300)

Error in UseMethod("grid.draw") :
no applicable method for 'grid.draw' applied to an object of class "list"

In spite of this error, the plot is still saved. However, the error stops the R pipeline I have written, and the other dozen graphs in my pipeline are not generated. Is there a way to resolve the issue of saving ggsurvplots without throwing an error?

kassambara · 2017-09-04T17:05:54Z

You can't use, the standard ggsave(), because ggsurvplot() always generates an object of class list, even if you set risk.table to FALSE. I think that I already suggested a solution to this issue. Please let me know if the solution works for you.

kassambara · 2017-09-04T17:08:13Z

The function ggpubr::ggexport() should work also for a list of ggplots, which are not supported by ggsave

jvanlunenburg · 2020-07-24T09:56:06Z

To anyone reading this, there is still no ggsave method for ggsurvplot objects.

kassambara · 2020-07-24T10:45:50Z

no, let's open this issue

chunjie-sam-liu · 2021-01-20T08:41:49Z

ggsave(
  filename ='os-plot.pdf',
  plot = print(os.plot, newpage = FALSE),
  device = 'pdf',
  path = 'data/output',
  width = 8,
  height = 9
)

Worked for me.

DKBurnsBresMed · 2021-07-30T11:16:31Z

This still does not work in version 0.4.9 e.g.:

ggsave(filename = "./debug/test_picture.png",plot = print(obj), device = "png")

produces a blank image for a simple Kaplan-Meier plot with number at risk table. generated with survminer.

Similarly the producing a plot to pdf method produces an unreadable pdf (error on loading).

UPDATE: the ggexport method does work, producing one blank image and one plot. The full plot is produced with the name (using the above example) test_picture002.png (001 is blank).

ggexport(filename = "./debug/test_picture.png",plot = obj, device = "png")

Hopefully useful for someone!

sstandage · 2021-08-17T15:26:16Z

Neither the ggsave nor the ggexport works well for me.

I'm getting blank output with ggsave whether I try to save as png or pdf. ggexport will allow me to save as a png, but for publication I need it in pdf. To get a pdf, I have to export using the RStudio utility and some elements are not rendered accurately. Any more ideas/changes?

adayim · 2021-10-08T17:36:43Z

There's a fix already, but you can use the code before it's been updated in the CRAN

grid.draw.ggsurvplot <- function(x){
  survminer:::print.ggsurvplot(x, newpage = FALSE)
}

Run this function before you save your plot using ggsave to save your plot.

Full working example

The code below should save the survival plot with risk table.

library("survival")
library("survminer")

fit <- survfit(Surv(time, status) ~ sex, data = lung)

p <- ggsurvplot(fit, risk.table = TRUE)

# add method to grid.draw
grid.draw.ggsurvplot <- function(x){
  survminer:::print.ggsurvplot(x, newpage = FALSE)
}

# Remember to pass object `p`.
ggsave("survival.png", plot = p, 
       dpi=300, width = 10, height = 7, units = "in")

adayim · 2021-12-18T23:46:58Z

@mleipzig
It works perfectly fine, I tried the all the code with the first code. You forgot to pass the plot object. The ggsurvplot function returns a ggsurvplot object, not a ggplot object and it will not write anything to last_plot(). Read ggsave function help thoroughly. I think you should correct your plot saving code:

ggsave("one_year_survival.tiff", plot = p, device="tiff", dpi=300, width = 20, height = 7, units = "in")

wiedenhoeft · 2022-01-13T12:00:04Z

None of these work for me, the best I get is the last plot being saved , i.e. the KM plot if there is no risk table, or the risk table alone.

wiedenhoeft · 2022-01-13T12:05:30Z

This works for me: ggsave(file="survival.pdf", plot=ggarrange(g$plot, g$table, nrow=2, ncol=1, heights=c(3,1)))

But this would have to be manually adapted based on the number of subplots. Also, the x-axes become misaligned.

This function is a workaround

save_ggsurvplot <- function(filename,
g,
rel_heights=c(3,1,1,1)){
nrplots=length(g)-2
ggsave(file=filename,
plot=ggarrange(plotlist=g[1:nrplots],
nrow=nrplots,
ncol=1,
align="v",
heights=rel_heights[1:nrplots]))
}

CorradoLanera · 2022-03-11T09:38:11Z

Maybe it could be possible to convert the res object evaluated in ggsurvplot::print.ggsurvplot to a proper ggplot object and return it.

In the meantime, the following behind-the-scenes workaround, seems working to me:

library("survival")
library("survminer")
#> Loading required package: ggplot2
#> Loading required package: ggpubr
#> 
#> Attaching package: 'survminer'
#> The following object is masked from 'package:survival':
#> 
#>     myeloma

fit <- survfit(Surv(time, status) ~ sex, data = lung)

With risk table

gg_risk <- ggsurvplot(fit, risk.table = TRUE)
risk_png <- tempfile("risk", fileext = ".png")
risk_png |>
  ggsave(
    plot = survminer:::.build_ggsurvplot(gg_risk)
  )
#> Saving 7 x 5 in image
if (!interactive() && requireNamespace("knitr")) {
  knitr::include_graphics(risk_png)
}

Without risk table

gg_norisk <- ggsurvplot(fit, risk.table = FALSE)
norisk_png <- tempfile("norisk", fileext = ".png")
norisk_png |>
  ggsave(
    plot = survminer:::.build_ggsurvplot(gg_norisk)
  )
#> Saving 7 x 5 in image
if (!interactive() && requireNamespace("knitr")) {
  knitr::include_graphics(norisk_png)
}

^{Created on 2022-03-11 by the reprex package (v2.0.1)}

Session info

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HuoJnx · 2022-03-11T10:18:24Z

Maybe it could be possible to convert the res object evaluated in ggsurvplot::print.ggsurvplot to a proper ggplot object and return it.

In the meantime, the following behind-the-scenes workaround, seems working to me:

library("survival")
library("survminer")
#> Loading required package: ggplot2
#> Loading required package: ggpubr
#> 
#> Attaching package: 'survminer'
#> The following object is masked from 'package:survival':
#> 
#>     myeloma

fit <- survfit(Surv(time, status) ~ sex, data = lung)

With risk table

gg_risk <- ggsurvplot(fit, risk.table = TRUE)
risk_png <- tempfile("risk", fileext = ".png")
risk_png |>
  ggsave(
    plot = survminer:::.build_ggsurvplot(gg_risk)
  )
#> Saving 7 x 5 in image
if (!interactive() && requireNamespace("knitr")) {
  knitr::include_graphics(risk_png)
}

Without risk table

gg_norisk <- ggsurvplot(fit, risk.table = FALSE)
norisk_png <- tempfile("norisk", fileext = ".png")
norisk_png |>
  ggsave(
    plot = survminer:::.build_ggsurvplot(gg_norisk)
  )
#> Saving 7 x 5 in image
if (!interactive() && requireNamespace("knitr")) {
  knitr::include_graphics(norisk_png)
}

Created on 2022-03-11 by the reprex package (v2.0.1)

Session info

Work for me, thanks!

kapsner · 2022-05-27T10:12:35Z

Both examples (from @adayim and @CorradoLanera) work for me (with argument risk.table=TRUE). It would be very nice, if one of these could be added to the exported functions for the next CRAN release.

kassambara closed this as completed Feb 19, 2017

kassambara reopened this Jul 24, 2020

mjakubczak linked a pull request Mar 18, 2021 that will close this issue

grid.draw method for ggsurvplot #522

Open

NikNakk mentioned this issue Jan 6, 2022

Make .buildggsurvplot an exported function #569

Open

ddsjoberg mentioned this issue Oct 7, 2022

Further instruction for saving files pharmaverse/ggsurvfit#107

Closed

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Saving ggsurvplot() #152

Saving ggsurvplot() #152

kassambara commented Feb 19, 2017

kassambara commented Feb 19, 2017 •

edited

VincentGuyader commented Aug 8, 2017

kassambara commented Aug 8, 2017

Phil-T commented Sep 4, 2017

kassambara commented Sep 4, 2017

kassambara commented Sep 4, 2017

jvanlunenburg commented Jul 24, 2020

kassambara commented Jul 24, 2020

chunjie-sam-liu commented Jan 20, 2021 •

edited

DKBurnsBresMed commented Jul 30, 2021 •

edited

sstandage commented Aug 17, 2021

adayim commented Oct 8, 2021 •

edited

adayim commented Dec 18, 2021 •

edited

wiedenhoeft commented Jan 13, 2022

wiedenhoeft commented Jan 13, 2022 •

edited

CorradoLanera commented Mar 11, 2022

HuoJnx commented Mar 11, 2022

With risk table

Without risk table

kapsner commented May 27, 2022

Saving ggsurvplot() #152

Saving ggsurvplot() #152

Comments

kassambara commented Feb 19, 2017

kassambara commented Feb 19, 2017 • edited

VincentGuyader commented Aug 8, 2017

kassambara commented Aug 8, 2017

Phil-T commented Sep 4, 2017

kassambara commented Sep 4, 2017

kassambara commented Sep 4, 2017

jvanlunenburg commented Jul 24, 2020

kassambara commented Jul 24, 2020

chunjie-sam-liu commented Jan 20, 2021 • edited

DKBurnsBresMed commented Jul 30, 2021 • edited

sstandage commented Aug 17, 2021

adayim commented Oct 8, 2021 • edited

Full working example

adayim commented Dec 18, 2021 • edited

wiedenhoeft commented Jan 13, 2022

wiedenhoeft commented Jan 13, 2022 • edited

CorradoLanera commented Mar 11, 2022

With risk table

Without risk table

HuoJnx commented Mar 11, 2022

With risk table

Without risk table

kapsner commented May 27, 2022

kassambara commented Feb 19, 2017 •

edited

chunjie-sam-liu commented Jan 20, 2021 •

edited

DKBurnsBresMed commented Jul 30, 2021 •

edited

adayim commented Oct 8, 2021 •

edited

adayim commented Dec 18, 2021 •

edited

wiedenhoeft commented Jan 13, 2022 •

edited