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March 3, 2020 23:35
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Trying to make something like Fig 5 from http://dx.doi.org/10.1136/bmjopen-2019-030215 using gridExtra, cowplot and survminer (ref: https://twitter.com/tmorris_mrc/status/1234946869362601984)
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| library(tidyverse) | |
| library(survminer) | |
| library(survival) | |
| library(cowplot) | |
| library(gridExtra) | |
| fit <- survfit(Surv(futime, fustat) ~ rx, data = ovarian) | |
| p1 <- ggsurvplot( | |
| fit, | |
| data = ovarian, | |
| size = 1, # change line size | |
| palette = c("#E7B800", "#2E9FDF"), # custom color palettes | |
| conf.int = TRUE, # Add confidence interval | |
| pval = TRUE, # Add p-value | |
| legend.labs = c("t1", "t2"), # Change legend labels | |
| ggtheme = theme_bw() # Change ggplot2 theme | |
| ) | |
| df <- surv_summary(fit, data = ovarian) | |
| t1 <- df %>% | |
| filter(rx == "1") %>% | |
| select(1,2,4,3) %>% | |
| mutate( | |
| Censored = cumsum(n.censor), | |
| Events = cumsum(n.event) | |
| ) %>% | |
| rename( | |
| At_risk = n.risk | |
| ) %>% | |
| select(-n.censor, -n.event) %>% | |
| t() %>% | |
| as_tibble( | |
| rownames = "item" | |
| ) %>% | |
| slice(2:4) | |
| t2 <- df %>% | |
| filter(rx == "2") %>% | |
| select(1,2,4,3) %>% | |
| mutate( | |
| Censored = cumsum(n.censor), | |
| Events = cumsum(n.event) | |
| ) %>% | |
| rename( | |
| At_risk = n.risk | |
| ) %>% | |
| select(-n.censor, -n.event) %>% | |
| t() %>% | |
| as_tibble( | |
| rownames = "item" | |
| ) %>% | |
| slice(2:4) | |
| tab1 <- tableGrob(t1, cols = NULL, rows = NULL) | |
| tab2 <- tableGrob(t2, cols = NULL, rows = NULL) | |
| plot_grid(p1$plot, tab1, tab2, | |
| labels = c("", "T1", "T2"), | |
| ncol = 1, rel_heights = c(6, 1, 1)) |
Author
jmcastagnetto
commented
Mar 3, 2020

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