Jens Sauer
439810a544
Replace the manual plotting definitions with the new function to reduce repitition.
66 lines
1.7 KiB
R
66 lines
1.7 KiB
R
# secMalASCT survival calculation
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#
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# License: GPL version 3
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# Jens Mathis Sauer (c) 2020
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library(survival)
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source("utils.R")
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secmal <- read.csv2("current.csv", header=TRUE)
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# Setup survival object
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surv_dx <- Surv(time = secmal$event_time_dx, event = secmal$event_status)
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surv_asct <- Surv(time = secmal$event_time_asct, event = secmal$event_status)
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# plot survival after diagnosis
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# scaled to years
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sma_plot_file("survival_dx.png", png,
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list(main = "Kaplan-Meier estimate for\nsecMalASCT study",
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sub = "Survival after diagnosis"),
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NULL,
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plot, survfit(surv_dx ~ 1),
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mark.time = TRUE,
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xscale = 365.25,
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xlab = "Years",
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ylab = "Survival")
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# One graph per sex
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sma_plot_file("survival_dx_sex.png", png,
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list(main = "Kaplan-Meier estimate for\nsecMalASCT study",
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sub = "Survival after diagnosis"),
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list(100, .9, c("Female", "Male"), lty = 2:3),
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plot, survfit(surv_dx ~ sex, data = secmal),
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mark.time = TRUE,
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xscale = 365.25,
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xlab = "Years",
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ylab = "Survival",
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lty = 2:3)
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# plot survival after diagnosis
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# scaled to years
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sma_plot_file("survival_asct.png", png,
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list(main = "Kaplan-Meier estimate for\nsecMalASCT study",
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sub = "Survival after transplantation"),
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NULL,
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plot, survfit(surv_asct ~ 1),
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mark.time = TRUE,
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xscale = 365.25,
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xlab = "Years",
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ylab = "Survival")
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# One graph per sex
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sma_plot_file("survival_asct_sex.png", png,
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list(main = "Kaplan-Meier estimate for\nsecMalASCT study",
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sub = "Survival after transplantation"),
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list(100, .9, c("Female", "Male"), lty = 2:3),
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plot, survfit(surv_asct ~ sex, data = secmal),
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mark.time = TRUE,
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xscale = 365.25,
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xlab = "Years",
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ylab = "Survival",
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lty = 2:3)
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