jsauer/secmalasct
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Merge branch 'survminer'

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* survminer:
  survival: Improve plots
  survival: Change plot function to ggsurvplot
This commit is contained in:
Jens Sauer 2020-11-17 14:04:07 +01:00
commit c087b40f5c
3 changed files with 38 additions and 21 deletions
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1
README.md
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@ -4,3 +4,4 @@ secMalASCT statistical analysis
R packages used
---------------
* tidyverse
* survminer

49
survival.R
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@ -4,6 +4,7 @@
# Jens Mathis Sauer (c) 2020
library(survival)
library(survminer)
source("utils.R")
secmal <- sma_load_data("current.csv")
@ -14,38 +15,46 @@ surv_asct <- Surv(time = secmal$event_time_asct, event = secmal$event_status)
# plot survival after diagnosis
sma_plot_surv_dx <- function() {
plot(survfit(surv_dx ~ 1), mark.time = TRUE, xscale = 365.25,
xlab = "Years", ylab = "Survival")
title("Kaplan-Meier estimate for\nsecMalASCT study",
"Survival after diagnosis")
ggsurvplot(survfit(surv_dx ~ 1), data = secmal, xscale = "d_y",
title = "Survival after diagnosis",
break.time.by = 5 * 365.25,
surv.median.line = "hv",
risk.table = "abs_pct",
ggtheme = theme_bw())
}
# plot survival after diagnosis per sex
sma_plot_surv_dx_sex <- function() {
plot(survfit(surv_dx ~ sex, data = secmal), mark.time = TRUE,
xscale = 365.25, xlab = "Years", ylab = "Survival",
lty = 2:3)
title("Kaplan-Meier estimate for\nsecMalASCT study",
"Survival after diagnosis")
legend(100, .9, c("Female", "Male"), lty = 2:3)
ggsurvplot(survfit(surv_dx ~ sex, data = secmal), data = secmal,
xscale = "d_y", title = "Survival after diagnosis",
legend.labs = c("Female", "Male"),
break.time.by = 5 * 365.25,
surv.median.line = "hv",
risk.table = "abs_pct",
ggtheme = theme_bw(),
pval = TRUE)
}
# plot survival after transplantation
sma_plot_surv_asct <- function() {
plot(survfit(surv_asct ~ 1), mark.time = TRUE, xscale = 365.25,
xlab = "Years", ylab = "Survival")
title("Kaplan-Meier estimate for\nsecMalASCT study",
"Survival after transplantation")
ggsurvplot(survfit(surv_asct ~ 1), data = secmal, xscale = "d_y",
title = "Survival after transplantation",
break.time.by = 5 * 365.25,
surv.median.line = "hv",
risk.table = "abs_pct",
ggtheme = theme_bw())
}
# plot survival after transplantation per sex
sma_plot_surv_asct_sex <- function() {
plot(survfit(surv_asct ~ sex, data = secmal), mark.time = TRUE,
xscale = 365.25, xlab = "Years", ylab = "Survival",
lty = 2:3)
title("Kaplan-Meier estimate for\nsecMalASCT study",
"Survival after transplantation")
legend(100, .9, c("Female", "Male"), lty = 2:3)
ggsurvplot(survfit(surv_asct ~ sex, data = secmal), data = secmal,
xscale = "d_y", title = "Survival after transplantation",
legend.labs = c("Female", "Male"),
break.time.by = 5 * 365.25,
surv.median.line = "hv",
risk.table = "abs_pct",
ggtheme = theme_bw(),
pval = TRUE)
}
#

9
utils.R
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@ -17,7 +17,14 @@ sma_plot_file <- function(fname, ftype, fun) {
# Open file for writing
ftype(filename = fname, width = 3000, height = 3000, res = 300)
fun()
#
# Write plot into variable, then printing it manually. This is
# needed to save plots from package "survminer" at the moment.
#
# See: https://github.com/kassambara/survminer/issues/152
#
p <- fun()
print(p)
# hide "null device 1" in garbage
garbage <- dev.off()