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Published
20 hours ago •
smouksassi
smouksassi
expand survival data geoms with geom_table_risk etc.
Hello,
I'm trying to achieve faceted KM plots. Your package makes it awesome easy with geom_XX syntax. Much easier than in other packages. It works for the geom_km (with the issue that it doesn't start the Y axis from 0 initially) and geom_band, yet it fails at geom_ticks for censored data. Let me show an example.
The data:
d <- structure(list(sex = structure(c(2L, 2L, 1L, 1L, 1L, 1L, 2L,
1L, 1L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 1L,
2L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 1L, 2L, 1L,
1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L,
1L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 1L, 2L,
2L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 2L,
1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 2L, 2L,
2L, 2L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 2L,
2L, 2L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 1L,
2L, 1L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 2L), .Label = c("Male",
"Female"), class = "factor"), RNR = structure(c(1L, 2L, 2L, 1L,
1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L,
2L, 2L, 2L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 1L,
2L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L,
1L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 1L,
1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 1L,
1L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L,
2L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 2L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 1L,
2L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 1L,
1L, 1L), .Label = c("Resectable", "Non-resectable"), class = "factor"),
TRT = structure(c(1L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L,
2L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 1L,
1L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L,
2L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 2L,
2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 2L,
2L, 2L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 2L,
1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L,
2L, 2L, 1L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 2L, 2L, 1L, 2L, 2L,
1L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L,
1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 2L,
2L, 2L, 1L, 2L, 2L), .Label = c("A", "B"), class = "factor"),
status = c(0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 1,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0,
0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,
0, 1, 0, 0, 1, 1, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,
0), time = c(16L, 97L, 98L, 52L, 78L, 52L, 51L, 100L, 52L,
50L, 96L, 45L, 27L, 57L, 52L, 100L, 96L, 100L, 99L, 49L,
100L, 100L, 100L, 96L, 100L, 19L, 93L, 52L, 98L, 100L, 100L,
53L, 100L, 100L, 97L, 98L, 100L, 100L, 96L, 98L, 98L, 100L,
98L, 52L, 51L, 95L, 50L, 98L, 100L, 99L, 100L, 100L, 49L,
99L, 97L, 100L, 50L, 100L, 52L, 100L, 99L, 43L, 49L, 45L,
52L, 94L, 49L, 98L, 57L, 24L, 52L, 98L, 50L, 80L, 50L, 100L,
48L, 82L, 46L, 46L, 10L, 52L, 51L, 95L, 18L, 97L, 100L, 97L,
44L, 100L, 96L, 100L, 96L, 99L, 52L, 100L, 95L, 99L, 97L,
100L, 97L, 55L, 52L, 100L, 97L, 100L, 100L, 97L, 76L, 100L,
100L, 100L, 100L, 52L, 52L, 93L, 100L, 45L, 47L, 98L, 100L,
93L, 98L, 100L, 46L, 52L, 46L, 49L, 52L, 50L, 52L, 52L, 100L,
100L, 99L, 42L, 45L, 54L, 99L, 81L, 52L, 97L, 13L, 18L, 96L,
95L, 99L, 99L, 100L, 99L)), row.names = c(NA, -150L), class = "data.frame")
Head:
> head(d)
sex RNR TRT status time
1 Female Resectable A 0 16
2 Female Non-resectable A 1 97
3 Male Non-resectable B 0 98
4 Male Resectable A 0 52
5 Male Resectable A 0 78
6 Male Non-resectable A 0 52
Plotting:
> ggplot(d, aes(time = time, status = status, color=sex)) +
+ geom_km()+
+ geom_kmticks()+
+ facet_grid(TRT ~ RNR)
Warnings:
and the output from the SurvMiner for a comparison:
EDIT:
OK, I fixed the issue on my own. The missing function comes from the package scales When I loaded it, it worked. Maybe you should pre-load it in your code? People may forget doing that.
> library(scales)
> ggplot(d, aes(time = time, status = status, color=sex)) +
+ geom_km()+
+ geom_kmticks()+
+ facet_grid(TRT ~ RNR)
> # no issue
Thanks I will keep it open to remind me to fix it in the next update. Please not that the Shiny app has a way to add a risk table with the median survival and CI but I am yet to implement it into a function.
Thank you very much.
Well, I don't use Shiny for anything, I rather needed it for a statistical report, where, indeed, I use the median + its CI. I add it easily with just 2 lines to the graph.
What I love the most in your approach is that:
- it perfectly integrates with the ggplot2-like syntax: geom_XX. I don't like monoliths like the SurvMiner. I'd love to have all those functionalities split into regular geom_ verbs.
geom_do_this + geom_do_that + geom_do_even_more. That's the way it should go rather than a_monstrous_function(with_dozens_of_parameters_not_easily_extendable)
- it enables the facet_XX functionality to any level handled by the ggplot2. SurvMiner allows me to use only 2 splitting factors. When I need 3 (which is typical in the pharmaceutical industry), I have a problem.
With your approach I can do the following easily:
or even more:
I think you could easily make a separate (that's important!) competing to the SurvMiner package for the ggplot2-based survival plotting, where each "unit functionality" is split into a corresponding geom_ or stat_ function (to expose all the important settings and parameters for advanced statisticians).
Exactly they way you do. It's really weird, it's been missing for so long time! I'd love to see it.
People, who do serious statistics (not just eye-catching presentations, with different fonts and colors), care more of the syntax-consistency and functionality.
Let me propose a few "geoms_" you might want to consider adding in the future:
- geom_km - done
- geom_cox - for covariate adjusted curves. With appropriate stat_ exposing the necessary parameters, like the way of calculating the baseline hazard, strata, cluster, estimator of variance, etc.
- geom_cmprsk - for competing risks (ideally both Fine-Gray or cause-specific-hazard)
- geom_recur - for recurrent events (e.g. Andersen-Gill extension of Cox)
- geom_atf (regression models, like the accelerated failure model, with survreg(), one of the most powerful tools in survival analysis, when the PH assumption fails)
- geom_ticks - done
- geom_band - done, but both for pointwise and simultaneous (for comparing entire curves) + appropriate stat_
- geom_compare_pairwise - adding a set of p-values for pairwise comparison of curves (with appropriate correction, can use the p.adjust() from R)
- geom_compare_overall - for the overall comparison of curves, like the Mantel-Hanshel log=rank, Peto-Peto modif. of the Gehan-Wilcoxon, Fleming-Harrington (with all the parameters exposed!), Gray (for competing risks). Those methods are important, as each looks at different time of changes between the curves. logrank looks at the middle, Gehan-Wilcoxon when the proportionality of hazards is violated (but curves do not cross) in that the failure times are log-normally distributed (with equal variances, as in the accelerated failure time model), indicating early differences between the survivals, Fleming-Harrington with p=0 and q=1 is used when the proportionality of hazards is violated (but curves do not cross) and late differences occur (based on the Nelson-Aalen estimator of the cumulative hazard). I use them all at work
- geom_cif (1-KM for unadjusted curves + covariate adjusted ones)
- geom_table - adds a table with number at risk, number of events and number of censored ones (could be split into geom_table_risk, geom_table_events, geom_table_censored)
- geom_zph - for Cox diagnostis, plotting the diagnostic plots from the cox.zph
- geom_median_time (with CI)
- geom_quantile_time (for other quantiles)
It's very important to make it a separate package. Why?
- it's easier to find (indexed by Google, placed in the appropriate R CRAN TaskViews). I would never think I will find geom_km in... ggquickeda package. I generally avoid anything that is "quick" (because it often means "rudimentary") and I don't like monoliths. I found this by a pure accident (and I'm happy!)
- for you it's easier to maintain, extend and validate with unit tests. Also - it's easier to publish.
- You risk less of being removed from the CRAN, if some of the external dependencies will fail at CRAN checking. Because smaller package means fewer dependencies
- you can add a nice hex-sticker to it, make dedicated vignette and web page. People don't have to read a huge documentation of the ggquickeda, if they need the survival analysis
- the more it's focused on a specific task, the better you control everything
- the geom_ functions don't mix with other tasks, from other areas.
I hope I encouraged you to consider starting this journey! You already did well with the basic geom_km. You saved my life, now I don't have to wrap the survfit with ggplot2 calls, having yours - ready to work :)
PS: Please consider adding your examples into the official ggplot2 extensions library! https://github.com/ggplot2-exts/gallery#adding-a-ggplot2-extension
Thanks for the valuable feedback. Initially this was written by @sachsmc and he gracefully accepted to be co-author and to include his code as part of ggquickeda. I do believe geom_km and friends is the most ggplot2 like amongst other solutions. I rewrote the ribbon code as at the time there was no stepped ribbon and also wrote it in a way that ggplotly would work. My sole purpose was to enable flexible km curves with facets grouping linetype etc. in my ggquickeda package . You bring a lot of points motivates me to re work on it as a separate package that ggquickeda depends on as you see there is value versus survminer GGally and others.
This is a great news! I hope the 2021 will be the year of birth of your new awesome package!
Let me show you what I did (quite quickly!) using your functions and a couple of additional tidyr-related coding (but no rocket-science here!)
MST stands for the median survival time. I could easily extend it by p-values and other stats, if space permits, but I will provide it in a separate table anyway. Just wanted to illustrate it. Sure, I could make something similar with the SurvMiner, but it would be limited only to 2 dimensions. With the flexibility of the ggplot2 faceting mechanism (enabled for the KM via your functions) I don't have to care of how many levels are needed by my client (now or in the future). I just sit, code and report.
@smouksassi and @sachsmc, please accept my deepest gratitude for your work!
PS: this is fake data, nothing secret is revealed here.
You may find useful a small piece of code, that translates the output of survfit into median survival times with grouping variables:
summary(fit)$table %>%
+ as.data.frame %>%
+ tibble::rownames_to_column() %>%
+ tidyr::separate(rowname, sep=",", into=paste0("gr_", c("column1", "column2", "column....."))) %>%
+ mutate(across(starts_with("gr_"), ~trimws(gsub(paste0(cur_column(), "="), "", .))))
with the following output (fit, and the processed fit):
PS: I will have to look later on the time conversion that SurvMiner can do for me in case I need other time units. For example:
.format_xticklabels <- function(labels, xscale){
# 1 year = 365.25 days
# 1 month = 365.25/12 = 30.4375 days
if(is.numeric(xscale)) xtrans <- 1/xscale
else
xtrans <- switch(xscale,
d_m = 12/365.25,
d_y = 1/365.25,
m_d = 365.25/12,
m_y = 1/12,
y_d = 365.25,
y_m = 12,
1
)
round(labels*xtrans,1)
}
@smouksassi Please look, how nicely things can be produced with your code. I put it here to encourage you to not abandon the survival functions in the future :) 🥇
Overall curves
fits <- lapply(c("sex", "age", "RNR", "TRT", "N2O"), function(strata)
survfit(as.formula( paste("Surv(time, status) ~", strata)), data=survival_data))
fit_summs <- lapply(fits, function(fit)
summary(fit, times = seq(0, 200, 50), extend = TRUE))
do.call(rbind,
lapply(fit_summs, function(fitsumm)
with(fitsumm, data.frame(value = strata,
time = time,
n.risk = n.risk,
n.censor = n.censor,
n.event = n.event)) %>%
mutate(value = trimws(gsub(".*=", "", value)))
)) -> surv_table
surv_table$value <- factor(surv_table$value)
do.call(rbind,
lapply(fit_summs, function(fitsumm)
fitsumm$table %>%
as.data.frame %>%
tibble::rownames_to_column() %>%
mutate(value = trimws(gsub(".*=", "", rowname))) %>%
mutate(time=NA, status=NA)
)) %>%
mutate(MST_line = row_number(),
MST = ifelse(is.na(median), "-",
as.character(median))) -> median_st
median_st$value <- factor(median_st$value)
survival_data %>%
tidyr::pivot_longer(cols = c(sex, age, N2O, RNR, TRT),
names_to = "variable",
values_to = "value") -> combined_data
(grA <- ggplot(combined_data, aes(time = time, status = status, color=value)) +
geom_km()+
geom_kmticks()+
theme_bw() +
theme(legend.position = "top") +
ggtitle("Progression-free survival of males and females",
subtitle = "by the treatment, resectable/non-resectable and N2/non-N2 groups") +
geom_text(data=median_st,
aes(x=0, y=0.06*MST_line, label=paste0(value, ": ")),
hjust = 0,
size=3,
show.legend = FALSE) +
geom_text(data=median_st,
aes(x=40, y=0.06*MST_line, label=MST),
hjust = 0,
size=3,
show.legend = FALSE) +
geom_text(data=median_st,
aes(x=0, y=(max(MST_line) + 1)*0.06,
label="Median Survival Time:"),
hjust = 0,
size=3,
show.legend = FALSE,
color="gray30") +
xlab("Time [months]") +
ylab("Survival probability") +
labs(color = "Strata") +
scale_y_continuous(labels = scales::percent_format(accuracy = 1)))
(grB <- ggplot(surv_table) +
geom_text(aes(x = time,
label = sprintf("%3d (%3d)", n.risk, n.event),
y=value),
size=2.8,
show.legend = FALSE) +
theme_bw() +
ylab(NULL) +
xlab(NULL) +
theme(panel.grid.minor.x = element_blank(),
panel.grid.major.x = element_blank()) +
ggtitle(label = "Number at risk and events over time",
subtitle = "#at risk (#events)") +
theme(plot.title = element_text(size=10),
plot.subtitle = element_text(size=8))
)
library(patchwork)
grA/grB
Curves split by appropriate factors (faceted):
current_survival_data <- survival_overall_data %>%
filter(sex != "Overall") %>%
droplevels()
fit <- survfit( Surv(time, status) ~ sex + TRT + RNR + N2O,
data = current_survival_data)
summ_fit <- summary(fit, times = c(0, 50, 100, 150, 200), extend = TRUE)
with(summ_fit,
data.frame(strata = strata,
time = time,
n.risk = n.risk,
n.censor = n.censor,
n.event = n.event)) %>%
tidyr::separate(strata,
sep=",",
into=c("sex", "TRT", "RNR", "N2O")) %>%
mutate(across(1:4, ~trimws(gsub(paste0(cur_column(), "="), "", .)))) %>%
mutate(status=NA) -> surv_table
# used to draw the median ST lines and print the numbers
summ_fit$table %>%
as.data.frame %>%
tibble::rownames_to_column() %>%
tidyr::separate(rowname, sep=",", into=c("sex", "TRT", "RNR", "N2O")) %>%
mutate(across(1:4, ~trimws(gsub(paste0(cur_column(), "="), "", .)))) %>%
mutate(MST_line = as.numeric(as.factor(sex)),
MST = ifelse(is.na(median), "-", as.character(median)),
time = NA,
status = NA) -> median_st
# The KM plot
ggplot(current_survival_data,
aes(time = time, status = status, color=sex)) +
facet_grid(TRT ~ RNR + N2O) +
geom_segment(data=median_st,
aes(x=0, xend=median, y=0.5, yend=0.5),
linetype="dashed",
size=1.05,
color="gray") +
geom_segment(data=median_st,
aes(x=median, xend=median, y=0, yend=0.5),
linetype="dashed",
size=1.05,
color="gray") +
geom_km()+
geom_kmticks()+
theme_bw() +
theme(legend.position = "top") +
ggtitle("Progression-free survival of males and females",
subtitle = "by the treatment, resectable/non-resectable and N2/non-N2 groups") +
geom_text(data=median_st,
aes(x=0, y=0.09*MST_line, label=paste0(sex, ":")),
hjust = 0, size=3,
show.legend = FALSE) +
geom_text(data=median_st,
aes(x=60, y=0.09*MST_line, label=MST),
hjust = 0, size=3,
show.legend = FALSE) +
geom_text(data=median_st,
aes(x=0, y=(max(MST_line)+1)*0.09, label="Med. Surv. Time:"),
hjust = 0, size=3,
show.legend = FALSE,
color="gray30") +
xlab("Time [months]") +
ylab("Survival probability") +
geom_rect(aes(xmin = -Inf, xmax = Inf, ymin = -Inf, ymax = 0),
fill="white", inherit.aes=FALSE) +
geom_hline(yintercept = 0, color = "grey", size=1) +
geom_text(data = surv_table, aes(x=time,
label =sprintf("%d", n.risk),
y=-0.1*as.numeric(as.factor(sex))),
size=2.8) +
scale_y_continuous(breaks = c(-.2, -.1, 0, .25, .5, .75, 1),
labels = c("Males", "Females", "0", "25%", "50%", "75%", "100%"),
limits = c(-0.2, 1)) +
# make some space from the left
xlim(-5, NA) +
theme(axis.text.y = element_text(colour = c(hue_pal()(2), rep("black", 5)),
size = c(7.5, 7.5, rep(8, 5))))
The data:
survival_data <- structure(list(age = structure(c(1L, 1L, 1L, 2L, 2L, 2L, 2L,
2L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 1L, 1L,
2L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L,
1L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 1L,
1L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 2L,
2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L,
2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 2L, 2L,
1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 1L,
1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 1L, 1L,
2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 2L), .Label = c("<65",
"<U+2265>65"), class = "factor"), sex = structure(c(1L, 2L, 1L,
1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L,
2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L,
2L, 2L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L,
2L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 2L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 2L,
1L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 1L,
2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 1L,
1L, 1L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L,
2L, 2L, 1L), .Label = c("Male", "Female"), class = "factor"),
N2O = structure(c(2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L,
1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 1L,
1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 1L,
2L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L,
2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L,
2L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 2L, 1L, 1L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L,
2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L,
1L, 1L, 2L, 1L, 2L), .Label = c("Overall", "N2"), class = "factor"),
RNR = structure(c(1L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 1L,
2L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 2L,
1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 1L,
1L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 1L,
2L, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 2L, 2L, 2L, 1L,
2L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 1L, 1L,
2L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 1L,
2L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L,
2L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L,
1L, 2L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 2L, 2L), .Label = c("Resectable", "Non-resectable"
), class = "factor"), TRT = structure(c(2L, 2L, 1L, 1L, 2L,
2L, 1L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 1L, 2L,
1L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 1L, 1L,
1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 2L,
1L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 1L,
2L, 2L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L,
1L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 1L,
2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 2L, 2L, 2L, 1L,
1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 2L,
1L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 2L,
2L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 2L), .Label = c("Surgery",
"CRT"), class = "factor"), time = c(81L, 80L, 179L, 136L,
1L, 180L, 2L, 91L, 185L, 37L, 2L, 186L, 80L, 199L, 78L, 3L,
4L, 83L, 96L, 8L, 77L, 35L, 38L, 118L, 163L, 140L, 195L,
172L, 127L, 3L, 2L, 83L, 31L, 6L, 125L, 38L, 125L, 3L, 197L,
36L, 127L, 119L, 181L, 4L, 3L, 176L, 128L, 169L, 12L, 167L,
195L, 3L, 125L, 89L, 1L, 195L, 38L, 134L, 1L, 177L, 1L, 40L,
191L, 148L, 190L, 188L, 159L, 80L, 175L, 188L, 2L, 36L, 88L,
78L, 1L, 86L, 3L, 185L, 35L, 2L, 3L, 193L, 37L, 84L, 193L,
177L, 2L, 3L, 1L, 73L, 38L, 2L, 173L, 38L, 84L, 197L, 49L,
196L, 186L, 3L, 1L, 36L, 89L, 46L, 2L, 4L, 152L, 2L, 166L,
92L, 185L, 175L, 79L, 175L, 5L, 182L, 156L, 186L, 35L, 200L,
36L, 38L, 190L, 131L, 60L, 131L, 1L, 79L, 4L, 143L, 75L,
197L, 81L, 118L, 196L, 86L, 194L, 192L, 36L, 1L, 196L, 125L,
138L, 89L, 198L, 86L, 37L, 77L, 1L, 146L), status = c(1,
0, 1, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0,
0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 1, 1, 1, 1,
0, 0, 1, 1, 1, 1, 0, 1, 0, 0, 1, 0, 1, 1, 1, 0, 1, 0, 0,
1, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 1, 0, 0, 1, 1, 1, 0,
0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0,
0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 1, 0, 1, 0, 0, 1, 0, 1, 1,
0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 1, 0, 1, 0, 1, 1, 0, 1, 0,
0, 0, 1, 0, 1, 0, 1, 1, 1, 0, 0, 0, 1, 0, 1, 1)), row.names = c(NA,
-150L), class = "data.frame")
levels(survival_data$age) <- c("<65", "\u226565")
## ---- survival_overall_data --------
srv_data_tmp <- survival_data
srv_data_tmp$sex <- "Overall"
data_ov_sex <- rbind(survival_data, srv_data_tmp)
#add overall age
srv_data_tmp <- data_ov_sex
srv_data_tmp$age <- "Overall"
data_ov_age <- rbind(data_ov_sex, srv_data_tmp)
#add overall RNR
srv_data_tmp <- data_ov_age
srv_data_tmp$RNR <- "Overall"
data_ov_RNR <- rbind(data_ov_age, srv_data_tmp)
#add overall TRT
srv_data_tmp <- data_ov_RNR
srv_data_tmp$TRT <- "Overall"
data_ov_TRT <- rbind(data_ov_RNR, srv_data_tmp)
survival_overall_data <- data_ov_TRT
rm(srv_data_tmp)
thanks this is awesome I hope I will have time to get around to this soon ! the above showcase why we need this code and package ! of course PR welcome
@smouksassi Hi! I don't know, if you finally decided to create a separate package for the survival analysis, but (to encourage you) I thought you might want to see, how flexible are the tools you made :) Let me show you an example - the final plot. Sure, there's nothing fancy about it - just ordinary KM. BUT, this can be faceted easily (to any level) without hacks, all components can be easily "commented out", no "million-parameters-big-function controlling everything". It's more in the tidyverse spirit.
Of course, I had to write some code to achieve that (e.g. the median survival time, the table with number of events, combined via patchwork package), but it was much easier with your "atomic" (I mean - simple, single-responsibility) functions km_XX, allowing me to get the basic plot and enhance it as I want, rather than hacking the survminer. That's why I loved your approach and why it would be great to have it separated - in the future :)
By the way, there's a smart way to exclude a KM band from a certain curve - like an "average" curve, which is just for informative purposes, but not for inference. I tried to achieve that by providing a separate filtered data, but it didn't work. I was wondering, if the km_bands could take an argument to decide to which curve the CI should be added. But, anyway, this can be achieved by assigning a "transparent color" to a certain "fill".
... + scale_fill_manual(values = c("Overall" = "transparent", "Resectable" = "green3", "Unresectable" = "red3"))
I have written a function that can produce the desired output with control on what to facet on and how to conduct logrank pvalue (grouping)
library(survival)
library(tidyverse)
library(ggquickeda)
library(ggrepel)
library(ggh4x)
ggkmandtable <- function(data = lung_long, # long format filter to Endpoint of choice
time = "time" , # long format filter to Endpoint of choice
status = "DV",
endpoint ="Endpoint",
groupvar1 = "Endpoint", #separate fit by endpoint and by expname
groupvar2 ="expname", # and up to two additional grouping
exposure_metrics = c("age","ph.karno"),
# exposures/covariates will be stacked into expname exptile
# i
exposure_metric_split = c("median","tertile","quartile","none"),
exposure_metric_soc_value = -99,
exposure_metric_plac_value = 0,
color_fill = "exptile",
linetype = "exptile",
xlab = "Time of follow_up",
ylab ="Overall survival probability",
nrisk_table_plot = TRUE,
nrisk_table_variables = c("n.risk"),#n.risk pct.risk n.event cum.n.event n.censor
nrisk_table_breaktimeby = NULL,
nrisk_table_textsize = 4,
nrisk_position_scaler = 0.2,
nrisk_position_dodge = 0.2,
nrisk_offset = 0,
nrisk_filterout0 = FALSE,
km_logrank_pvalue = FALSE,
km_trans ="identity" ,#"identity","event","cumhaz","cloglog")
km_ticks = TRUE,
km_band = TRUE,
km_conf_int = 0.95,
km_conf_type = "log", #c("none" , "plain", "log" ,"log-log","logit"),
km_conf_lower = "usual", #c("peto" , "modified", "usual"),
km_median = "none", #medianci,median none
km_yaxis_position = c("left"),#"right
facet_formula = NULL,
facet_ncol = NULL,
facet_strip_position = c("top","top","top","top")
) {
timevar <- time
statusvar <- status
endpointinputvar <- endpoint
groupvar1inputvar <- groupvar1
groupvar2inputvar <- groupvar2
colorinputvar <- if (color_fill !="none") color_fill else NULL
fillinputvar <- if (color_fill !="none") color_fill else NULL
linetypeinputvar <- if (linetype !="none") linetype else NULL
survformula <- paste( "Surv","(",timevar,",",statusvar,")",sep="")
facet_formula <- if (is.null(facet_formula) ) stats::as.formula( paste("~",groupvar1inputvar,"+",groupvar2inputvar)) else
stats::as.formula(facet_formula)
exposure_metric_split <- match.arg(exposure_metric_split)
data <- data %>%
mutate(none = "none") # needed when no metric are chosen
data.long <- data %>%
gather(expname,expvalue,!!!exposure_metrics) %>%
group_by(expname,!!endpoint)
if(exposure_metric_split=="none") {
data.long <- data.long %>%
mutate(exptile = case_when(
#expvalue == exposure_metric_soc_value ~ "SOC",
#expvalue == exposure_metric_plac_value ~ "Placebo",
#expvalue > exposure_metric_plac_value ~ "all"))
expvalue == exposure_metric_soc_value ~ NA,
expvalue == exposure_metric_plac_value ~ NA,
expvalue > exposure_metric_plac_value ~ expvalue))
}
if(exposure_metric_split=="quartile") {
data.long <- data.long %>%
mutate(
Q25 = quantile(expvalue[!expvalue %in% c(exposure_metric_soc_value,
exposure_metric_plac_value)], 0.25, na.rm=TRUE),
Q50 = quantile(expvalue[!expvalue %in% c(exposure_metric_soc_value,
exposure_metric_plac_value)], 0.50, na.rm=TRUE),
Q75 = quantile(expvalue[!expvalue %in% c(exposure_metric_soc_value,
exposure_metric_plac_value)], 0.70, na.rm=TRUE)) %>%
mutate(exptile = case_when(
expvalue == exposure_metric_soc_value ~ "SOC",
expvalue == exposure_metric_plac_value ~ "Placebo",
expvalue > exposure_metric_plac_value &
expvalue <= Q25 ~ "Q1",
expvalue > Q25 & expvalue <= Q50 ~ "Q2",
expvalue > Q50 & expvalue <= Q75 ~ "Q3",
expvalue > Q75 ~ "Q4"))
}
if(exposure_metric_split=="tertile") {
data.long <- data.long %>%
mutate(
Q33 = quantile(expvalue[!expvalue %in% c(exposure_metric_soc_value,
exposure_metric_plac_value)], 1/3, na.rm=TRUE),
Q66 = quantile(expvalue[!expvalue %in% c(exposure_metric_soc_value,
exposure_metric_plac_value)], 2/3, na.rm=TRUE)) %>%
mutate(exptile = case_when(
expvalue == exposure_metric_soc_value ~ "SOC",
expvalue == exposure_metric_plac_value ~" Placebo",
expvalue > exposure_metric_plac_value &
expvalue <= Q33 ~ "T1",
expvalue > Q33 & expvalue <= Q66 ~ "T2",
expvalue > Q66 ~ "T3"))
}
if(exposure_metric_split=="median") {
data.long <- data.long %>%
mutate(
Q50 = quantile(expvalue[!expvalue %in% c(exposure_metric_soc_value,
exposure_metric_plac_value)], 0.5, na.rm=TRUE)) %>%
mutate(exptile = case_when(
expvalue == exposure_metric_soc_value ~"SOC",
expvalue == exposure_metric_plac_value ~"Placebo",
expvalue > 0 & expvalue <= Q50 ~ "M1",
expvalue > Q50 ~ "M2"))
}
data.long$exptile2 <- data.long$exptile
#we generate a curve by the combination of all these inputs removing duplicates and none
listvars <- unique(c(endpointinputvar,colorinputvar,fillinputvar,linetypeinputvar,groupvar1,groupvar2))
listvars <- listvars[!is.element(listvars,c("none",".")) ]
listvars <- listvars[!duplicated(listvars) ]
if ( length(listvars) ==0 ){
f <- as.formula(paste(survformula, "1", sep = " ~ "))
}
if ( length(listvars) >0 ){
f <- as.formula(paste(survformula, paste(listvars, collapse = " + "), sep = " ~ "))
}
surv_object <- eval(bquote( survfit( .(f) , data.long) ))
if (is.null(nrisk_table_breaktimeby) ||
nrisk_table_breaktimeby == '' ||
is.na(nrisk_table_breaktimeby)){
ggsurv <- survminer::ggsurvplot(surv_object,
data.long,risk.table = TRUE,
ggtheme = theme_bw())
} else {
ggsurv <- survminer::ggsurvplot(surv_object,
data.long,risk.table = TRUE,
break.time.by = nrisk_table_breaktimeby,
ggtheme = theme_bw())
}
if(km_logrank_pvalue){ #log rank does not group by color_fill, linetype exptile
loopvariables <- unique(c(endpointinputvar,"expname",groupvar1,groupvar2))
loopvariables <- loopvariables[!loopvariables%in% "exptile"]
listvars2 <- listvars[!listvars%in% loopvariables]
if ( length(listvars2) ==0 ){
f2 <- as.formula(paste(survformula, "1", sep = " ~ "))
}
if ( length(listvars2) >0 ){
f2 <- as.formula(paste(survformula, paste(listvars2, collapse = " + "), sep = " ~ "))
}
survfit_by_endpoint <- list()
logrank_test_by_endpoint <- list()
data.long <- unite(data.long,"loopvariable", !!!loopvariables, remove = FALSE)
for (i in unique(data.long[,"loopvariable"]) %>%
pull() %>%
as.character() ) {
survregdata<- data.long %>%
filter(.data[["loopvariable"]] ==i)
survfit_by_endpoint_fit <- eval(bquote( survfit( .(f2) , survregdata) ))
survfit_by_endpoint[[i]] <- survfit_by_endpoint_fit
logrank_test_by_endpoint_fit <- survminer::surv_pvalue(survfit_by_endpoint_fit, method = "1",
data=survregdata)
logrank_test_by_endpoint_fit[,"loopvariable"] <- i
logrank_test_by_endpoint[[i]] <- logrank_test_by_endpoint_fit
}
logrank_test_by_endpoint <- enframe(logrank_test_by_endpoint) %>%
unnest(cols = c(value))
logrank_test_by_endpoint <- logrank_test_by_endpoint %>%
separate(loopvariable, into = loopvariables,
sep="_",extra = "merge"
)
#print(listvars2)
#print(f2)
#print(logrank_test_by_endpoint)
}
#print(listvars)
#print(f)
risktabledata <- ggsurv$table$data
#print(risktabledata)
if(!is.null(surv_object$strata)){
variables <- survminer:::.get_variables(risktabledata$strata, surv_object, data.long)
for(variable in variables) {
risktabledata[[variable]] <- survminer:::.get_variable_value(variable,risktabledata$strata, surv_object, data.long)
}
}
if(nrisk_filterout0){
risktabledata <- risktabledata %>%
filter(n.risk > 0)
}
if(!is.null(nrisk_table_variables) && (length(as.vector(nrisk_table_variables)) > 0) &&
all(nrisk_table_variables != "")){
risktabledatag<- gather(risktabledata,key,value, !!!nrisk_table_variables , factor_key = TRUE)
risktabledatag$keynumeric<- - nrisk_position_scaler* as.numeric(as.factor(risktabledatag$key)) + nrisk_offset
}
if(is.null(nrisk_table_variables) || all(nrisk_table_variables == "") ) {
risktabledatag<- gather(risktabledata,key,value, n.risk, factor_key = TRUE)
risktabledatag$keynumeric<- - nrisk_position_scaler* as.numeric(as.factor(risktabledatag$key)) + nrisk_offset
}
if (km_median!="none"){
if(!is.null(surv_object$strata) || is.matrix(surv_object$surv)) {
.table <- as.data.frame(summary(surv_object)$table)
} else {
.table <- t(as.data.frame(summary(surv_object)$table))
rownames(.table) <- "(all)"
}
surv_median <- as.vector(.table[,"median"])
dfmedian <- data.frame(x1 = surv_median,
x2 = surv_median,
x1lower = as.vector(.table[,"0.95LCL"]),
x1upper = as.vector(.table[,"0.95UCL"]),
y1 = rep(0, length(surv_median)),
y2 = rep(0.5, length(surv_median)),
strata = survminer:::.clean_strata(rownames(.table)))
if(!is.null(surv_object$strata)){
variables <- survminer:::.get_variables(dfmedian$strata, surv_object, data.long)
for(variable in variables) {
dfmedian[[variable]] <- survminer:::.get_variable_value(variable, dfmedian$strata, surv_object, data.long)
}
}
}
plotkm0 <- ggplot(data.long,aes_string(time = time,status = status,
color = colorinputvar, fill = fillinputvar,
linetype = linetypeinputvar))+
geom_line(stat = "km",trans = km_trans)
if(km_band){
plotkm00 <- plotkm0 +
geom_ribbon(stat="kmband",alpha=0.2,color="transparent",
conf.int = km_conf_int,
conf.type = km_conf_type,
conf.lower = km_conf_lower,
error = "greenwood",
trans = km_trans)
}
if(!km_band){
plotkm00 <- plotkm0
}
if(km_ticks){
plotkm000 <- plotkm00 +
geom_kmticks(trans = km_trans)
}
if(!km_ticks){
plotkm000 <- plotkm00
}
if(nrisk_table_plot) {
plotkm1 <- plotkm000 +
geom_text(data=risktabledatag,
aes(x=time,label=value,y=keynumeric,time=NULL,status=NULL ),
show.legend = FALSE,
size= nrisk_table_textsize,
position = ggstance::position_dodgev(height =nrisk_position_dodge)
)+
geom_hline(yintercept = -nrisk_position_scaler *unique(c(1,(as.numeric(as.factor(
risktabledatag$key))+1 )) ) + (abs(nrisk_position_dodge)/2 ) + nrisk_offset
)
}
if(!nrisk_table_plot) {
plotkm1 <- plotkm0
}
if(km_median=="table"){
plotkm1m <- plotkm1 +
geom_text(data=dfmedian %>% mutate(none="none"),
aes(x=0, y=(max(as.numeric(as.factor(get(!!color_fill))))+1)*0.09,
label="Med. Surv. Time:"),
hjust = 0, size=3,
show.legend = FALSE,
color="gray30",inherit.aes = FALSE) +
geom_text(data=dfmedian %>% mutate(none="none",
"{timevar}" := NA,
"{statusvar}" := NA),
aes(x=0, y=0.09*as.numeric(as.factor(get(!!color_fill))),
label=paste0(get(!!color_fill), ":")),
hjust = 0, size=3,
show.legend = FALSE,inherit.aes = TRUE) +
geom_text(data=dfmedian %>% mutate(none="none",
"{timevar}" := NA,
"{statusvar}" := NA),
aes(x=60, y=0.09*as.numeric(as.factor(get(!!color_fill))),
label=ifelse(is.na(x1), "-",as.character(x1))),
hjust = 0, size=3,
show.legend = FALSE,inherit.aes = TRUE)
}
if(km_median=="medianci"){
plotkm1m <- plotkm1 +
geom_label_repel(data = dfmedian, aes(x= x1 , y= y2 ,label =sprintf("%#.3g (%#.3g, %#.3g)",x1,x1lower,x1upper),
status=NULL,time=NULL),show.legend = FALSE,
label.size = NA, direction="both",fill="white",
segment.color="black",nudge_y = -0.1,segment.size = 0.5,
alpha = 0.5,label.padding=.1, force = 5,
na.rm=TRUE,
seed = 1234) +
geom_label_repel(data = dfmedian, aes(x= x1 , y= y2 ,label =sprintf("%#.3g (%#.3g, %#.3g)",x1,x1lower,x1upper),
status=NULL,time=NULL),show.legend = FALSE,
label.size = NA,direction="both",
nudge_y = -0.1,segment.size = 0.5,
arrow = arrow(length = unit(0.03, "npc"), type = "closed", ends = "first"),
alpha = 1,label.padding=.1, force = 5,
na.rm=TRUE,
fill = NA,
seed = 1234)
}
if(km_median=="median"){
plotkm1m <- plotkm1 +
geom_label_repel(data = dfmedian, aes(x= x1 , y= y2 ,label = sprintf("%#.3g",x1), status=NULL,time=NULL),show.legend = FALSE,
label.size = NA, direction="both",fill="white",
segment.color="black",nudge_y = -0.1,segment.size = 0.5,
alpha = 0.5,label.padding=.1, force = 5,
na.rm=TRUE,
seed = 1234) +
geom_label_repel(data = dfmedian, aes(x= x1 , y= y2 ,label =sprintf("%#.3g",x1),
status=NULL,time=NULL),show.legend = FALSE,
label.size = NA,direction="both",
nudge_y = -0.1,segment.size = 0.5,
arrow = arrow(length = unit(0.03, "npc"), type = "closed", ends = "first"),
alpha = 1,label.padding=.1, force = 5,
na.rm=TRUE,
fill = NA,
seed = 1234)
}
if(km_median=="none"){
plotkm1m <- plotkm1
}
plotkm2 <- plotkm1m +
facet_nested_wrap(facet_formula,ncol= facet_ncol ,
strip = strip_split(position=facet_strip_position))+
scale_y_continuous(position = km_yaxis_position,
breaks =c(unique(risktabledatag$keynumeric),
c(0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1) ),
labels= c(as.vector(unique(risktabledatag$key)),
c("0","10","0.2","0.3","0.4","0.5","0.6","0.7","0.8","0.9","1") ),
expand = expansion(mult=c(0.01,0.01),
add =c(0, 0)))+
scale_x_continuous( breaks =c(unique(risktabledatag$time))) +
theme_bw()+
theme(legend.position = "top",strip.placement = "outside",
axis.title.y = element_blank())+
labs(color="",fill="",linetype="",
x = xlab,y = ylab)
if(km_logrank_pvalue){
plotkm3 <- plotkm2 +
geom_text(data=logrank_test_by_endpoint,
aes(x=-Inf,y=Inf,label=pval.txt),vjust=1,hjust=0,
inherit.aes = FALSE)
plotkm <- plotkm3
}
if(!km_logrank_pvalue) {
plotkm <- plotkm2
}
plotkm
}
Example
library(tidyverse)
library(patchwork)
library(ggquickeda)
library(patchwork)
library(ggh4x)
library(survival)
library(survminer)
source("ggkmandtable.R")
# see comments above to dput survival_overall_data
current_survival_data <- survival_overall_data %>%
filter(sex != "Overall") %>%
droplevels()
ggkmandtable (data = current_survival_data,
time= "time",
status ="DV",
exposure_metrics =c("none"),
exposure_metric_split = "none",
color_fill = "sex",
linetype = "TRT",
groupvar1 = "RNR",
groupvar2 = "N2O",
xlab = "Time of follow_up",
ylab ="Overall survival probability",
nrisk_table_variables = c("n.censor"),
km_median = "table",
km_band = FALSE,
nrisk_table_breaktimeby = NULL,
facet_formula ="~TRT+RNR+N2O",
facet_ncol = 6,
facet_strip_position = c("right","top","top") )