axes.offset and risk table alignment

[dmartinffm]

Expected behavior

Risk tables should align to X axis ticks of the plot when using axes.offset=FALSE

Actual behavior

Tables are not aligned to plot

Steps to reproduce the problem

Use risk.table=TRUE and axes.offset=FALSE

session_info()

# please paste here the result of
devtools::session_info()

Session info ------------------------------------------------------------------
setting value
version R version 3.3.1 (2016-06-21)
system x86_64, darwin13.4.0
ui RStudio (1.0.136)
language (EN)
collate de_DE.UTF-8
tz Europe/Berlin
date 2017-07-11

Packages ----------------------------------------------------------------------
package * version date source
assertthat 0.2.0 2017-04-11 CRAN (R 3.3.2)
base * 3.3.1 2016-06-24 local
bindr 0.1 2016-11-13 cran (@0.1)
bindrcpp * 0.2 2017-06-17 cran (@0.2)
broom 0.4.2 2017-02-13 CRAN (R 3.3.2)
cmprsk 2.2-7 2014-06-17 CRAN (R 3.3.0)
colorspace 1.3-2 2016-12-14 CRAN (R 3.3.2)
data.table 1.10.4 2017-02-01 CRAN (R 3.3.1)
datasets * 3.3.1 2016-06-24 local
devtools 1.13.2 2017-06-02 CRAN (R 3.3.2)
digest 0.6.12 2017-01-27 CRAN (R 3.3.2)
dplyr * 0.7.1 2017-06-22 cran (@0.7.1)
forcats 0.2.0 2017-01-23 CRAN (R 3.3.2)
foreign 0.8-69 2017-06-21 CRAN (R 3.3.2)
ggplot2 * 2.2.1 2016-12-30 CRAN (R 3.3.2)
ggpubr * 0.1.4 2017-06-28 cran (@0.1.4)
glue 1.1.1 2017-06-21 cran (@1.1.1)
graphics * 3.3.1 2016-06-24 local
grDevices * 3.3.1 2016-06-24 local
grid 3.3.1 2016-06-24 local
gridExtra 2.2.1 2016-02-29 CRAN (R 3.3.0)
gtable 0.2.0 2016-02-26 CRAN (R 3.3.0)
haven * 1.1.0 2017-07-09 CRAN (R 3.3.2)
hms 0.3 2016-11-22 CRAN (R 3.3.2)
km.ci 0.5-2 2009-08-30 CRAN (R 3.3.0)
KMsurv 0.1-5 2012-12-03 CRAN (R 3.3.0)
knitr 1.16 2017-05-18 CRAN (R 3.3.2)
lattice 0.20-35 2017-03-25 CRAN (R 3.3.2)
lazyeval 0.2.0 2016-06-12 CRAN (R 3.3.0)
magrittr * 1.5 2014-11-22 CRAN (R 3.3.0)
Matrix 1.2-10 2017-04-28 CRAN (R 3.3.2)
memoise 1.1.0 2017-04-21 CRAN (R 3.3.2)
methods * 3.3.1 2016-06-24 local
mnormt 1.5-5 2016-10-15 CRAN (R 3.3.0)
munsell 0.4.3 2016-02-13 CRAN (R 3.3.0)
nlme 3.1-131 2017-02-06 CRAN (R 3.3.2)
parallel 3.3.1 2016-06-24 local
pkgconfig 2.0.1 2017-03-21 cran (@2.0.1)
plyr 1.8.4 2016-06-08 CRAN (R 3.3.0)
psych 1.7.5 2017-05-03 CRAN (R 3.3.1)
purrr 0.2.2.2 2017-05-11 CRAN (R 3.3.2)
R6 2.2.2 2017-06-17 cran (@2.2.2)
Rcpp 0.12.11 2017-05-22 CRAN (R 3.3.2)
readr 1.1.1 2017-05-16 CRAN (R 3.3.2)
reshape2 1.4.2 2016-10-22 CRAN (R 3.3.0)
rlang 0.1.1 2017-05-18 CRAN (R 3.3.2)
scales 0.4.1 2016-11-09 CRAN (R 3.3.2)
splines 3.3.1 2016-06-24 local
stats * 3.3.1 2016-06-24 local
stringi 1.1.5 2017-04-07 CRAN (R 3.3.2)
stringr 1.2.0 2017-02-18 CRAN (R 3.3.2)
survival * 2.41-3 2017-04-04 CRAN (R 3.3.2)
survminer * 0.4.0.999 2017-07-11 Github (bea688c)
survMisc 0.5.4 2016-11-23 CRAN (R 3.3.2)
tibble 1.3.3 2017-05-28 CRAN (R 3.3.2)
tidyr 0.6.3 2017-05-15 CRAN (R 3.3.2)
tools 3.3.1 2016-06-24 local
utils * 3.3.1 2016-06-24 local
withr 1.0.2 2016-06-20 CRAN (R 3.3.0)
xtable 1.8-2 2016-02-05 CRAN (R 3.3.0)
zoo 1.8-0 2017-04-12 CRAN (R 3.3.2)

[kassambara]

Hi,

I'm out of office and have limited access to my e-mail. I will be able to check this on jully 17th.

Thank you

[x-ray90]

I'm having the same problem. I really would like to avoid using the axis offset since I find it not precicely representing the data. However with this issue I am also prevented from using risk tables (since the number at risk does not align with the breaks of the x-axis).

[x-ray90]

Is there maybe a hack to cancel the axis offset for the risk table? Would be great to have graph and risk table align...

[IsaSmall]

Hi,

Is this problem already solved? I'm finishing up a paper and it would be great if I could have them aligned (using axes.offset=FALSE).

Thanks

[kassambara]

Fixed now, thanks.

library(survival)
library(survminer)
data(lung)
fit <- survfit(Surv(time, status) ~sex, data = lung)
ggsurvplot(fit, risk.table = TRUE, axes.offset = FALSE,
           xlim = c(0, 1050))

[IsaSmall]

Hi Kassambara,

Thank you for the quick response. But, it didn't work for me or maybe I am doing something wrong...

fit <- survfit(Surv(IG, Obito) ~ Tratamento, data = neos)

ggsurv<- ggsurvplot(fit, data = neos,
pval = TRUE, # Add p-value & method name
pval.method = FALSE,
pval.size = 4,
pval.coord = c(2, 0.1),
legend.title = " ",
legend.labs = c("A", "B"),
palette = "lancet",
surv.median.line = "hv",
risk.table = TRUE,
risk.table.height = 0.20,
risk.table.pos = "out",
risk.table.fontsize = 4,
cumevents = FALSE,
tables.height = 0.15,
tables.theme = theme_cleantable(),
tables.y.text = FALSE,
xlim = c(0,96),
xlab = "Follow-up (months)",
axes.offset = FALSE,
break.time.by = 12,
yslim = c(0,100),
ylab = "Overall survival",
break.y = 0.10,
font.y= c(12, "plain"),
font.x = c(12, "plain"),
font.tickslab = c(9, "plain"),
surv.scale = "percent"
)
ggsurv$table <- ggsurv$table +
theme(plot.title = element_text(size = 10, color = "black", face = "plain"))
ggsurv

[kassambara]

You need to install the latest developmental version of survminer

[IsaSmall]

Great! Thank you very much, @kassambara!