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ggtheme() not supported when using list of survfit objects in ggsurvplot(). #278

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PhonePong opened this Issue Jan 10, 2018 · 1 comment

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PhonePong commented Jan 10, 2018

Expected behavior

Ability to select theme of ggplot using ggtheme() argument in ggsurvplot() function.

Actual behavior

No theme change with input.

Steps to reproduce the problem

# Split this data (explained below)
colon.sex0 <- colon[!(colon$sex %in% 1), ]
colon.sex1 <- colon[!(colon$sex %in% 0), ]

# Create Kaplan-Maier and Cox Proportional Hazard estimate where sex = 0
sex0.kaplan <- survfit(Surv(time, status) ~ sex, data = colon.sex0)
sex0.cox <- survfit(coxph(Surv(time, status) ~ sex, data = colon.sex0))
# Make a list for comparison
sex0.fits <- list(Kaplan = sex0.kaplan, Cox = sex0.cox)

# Same, but where sex = 1
sex1.kaplan <- survfit(Surv(time, status) ~ sex, data = colon.sex1)
sex1.cox <- survfit(coxph(Surv(time, status) ~ sex, data = colon.sex1))
# Make a list for comparison
sex1.fits <- list(Kaplan = sex1.kaplan, Cox = sex1.cox)

# Compare all
all.fits <- list(Kaplan.0 = sex0.kaplan, Cox.0 = sex0.cox, Kaplan.1 = sex1.kaplan, Cox.1 = sex1.cox)

# Plots
ggsurv.sex0 <- ggsurvplot(sex0.fits, fun = "event", ggtheme = theme_gray(), conf.int = TRUE, legend = "right", combine = TRUE, linetype = c(1, 2), palette = "strata", censor = FALSE)
sex0.plot <- ggsurv.sex0 + ggtitle("THIS IS NOT theme_gray()") + labs(subtitle = "but I wish it was...", x ="TIME", y = "CDF")

ggsurv.sex1 <- ggsurvplot(sex1.fits, fun = "event", ggtheme = theme_dark(), conf.int = TRUE, legend = "right", combine = TRUE, linetype = c(1, 2), palette = "strata", censor = FALSE)
sex1.plot <- ggsurv.sex1 + ggtitle("THIS IS NOT theme_dark()") + labs(subtitle = "but I wish it was...", x ="TIME", y = "CDF")

ggsurv.all <- ggsurvplot(all.fits, fun = "event", ggtheme = theme_void(), conf.int = TRUE, legend = "right", combine = TRUE, linetype = c(1, 2, 1, 2), palette = "strata", censor = FALSE)
all.plot <- ggsurv.all + ggtitle("THIS IS NOT theme_void()") + labs(subtitle = "but I wish it was...", x ="TIME", y = "CDF")
Should Be theme_gray Should Be theme_dark Should Be theme_void
Showing NOT theme_gray() Showing NOT theme_dark() Showing NOT theme_void()

The reason I separate the colon data is because when I run

# Again, create Kaplan-Maier and Cox Proportional Hazard estimates but using all data
kaplan.sex <- survfit(Surv(time, status) ~ sex, data = colon)
cox.sex <- survfit(coxph(Surv(time, status) ~ sex, data = colon))

# Make list for comparison
fits.sex <- list(sex.km = kaplan.sex, sex.cox = cox.sex)

It creates an undesired result of creating cox estimate for all the data (when I would like to see separate estimates).

# Plot
ggsurv.sex <- ggsurvplot(fits.sex, colon, fun = "event", conf.int = TRUE, legend = "right", palette = c("jco"), combine = TRUE, linetype = c(1,2,3))
sex.plot <- ggsurv.sex + ggtitle("THIS IS NOT WHAT I WANTED") + labs(subtitle = "but I wish it was...", x ="TIME", y = "CDF")
Undesired Output
Undesired Result

Awesome package by the way =D
-jim

session_info()

R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] splines   grid      stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] bindrcpp_0.1         bshazard_1.0         Epi_2.19            
 [4] survPresmooth_1.1-10 MASS_7.3-47          scales_0.4.1        
 [7] stringr_1.2.0        taRifx_1.0.6         RCurl_1.95-4.8      
[10] bitops_1.0-6         XML_3.98-1.9         gridExtra_2.2.1     
[13] data.table_1.10.4    survminer_0.4.0      survMisc_0.5.4      
[16] survival_2.41-3      ggpubr_0.1.4         magrittr_1.5        
[19] ggplot2_2.2.1        xlsx_0.5.7           xlsxjars_0.6.1      
[22] rJava_0.9-8         

loaded via a namespace (and not attached):
 [1] zoo_1.8-0         purrr_0.2.2.2     reshape2_1.4.2    etm_0.6-2        
 [5] lattice_0.20-35   colorspace_1.3-2  rlang_0.1.1       foreign_0.8-67   
 [9] glue_1.1.0        bindr_0.1         plyr_1.8.4        munsell_0.4.3    
[13] gtable_0.2.0      ggsci_2.7         psych_1.7.5       labeling_0.3     
[17] knitr_1.16        parallel_3.4.0    broom_0.4.2       Rcpp_0.12.11     
[21] xtable_1.8-2      cmprsk_2.2-7      km.ci_0.5-2       mnormt_1.5-5     
[25] digest_0.6.12     stringi_1.1.5     dplyr_0.7.0       KMsurv_0.1-5     
[29] numDeriv_2016.8-1 cowplot_0.7.0     tools_3.4.0       lazyeval_0.2.0   
[33] tibble_1.3.3      tidyr_0.6.3       Matrix_1.2-9      assertthat_0.2.0 
[37] R6_2.2.2          nlme_3.1-131      compiler_3.4.0

#204

kassambara added a commit that referenced this issue Jan 10, 2018

@kassambara

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kassambara commented Jan 10, 2018

fixed now; Thank you for this clear reproducible example

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