both figures for paper, bar plot of failure plus kaplan surv curve

library(ggplot2);library(readxl);library(randomForest);library(caret);library(epitools);library(survival);library(ggfortify); library(survminer)

df <- read.csv("shunt_figures_data.csv", header = TRUE)

#yes = 1, no = 0
df$Failure.within.first.year.after.surgery <- ifelse(df$Failure.within.first.year.after.surgery=='y', 1, 0)

df$Gestational.Age.at.First.Shunt..in.Days.<- as.numeric(df$Gestational.Age.at.First.Shunt..in.Days.)
df$GA_S <- df$Gestational.Age.at.First.Shunt..in.Days./7  

#less than 40 = 0
#greater than 40 = 1
df$GAlessthan40 <- ifelse(df$GA_S<40,0,1)

df$weeks_fail<- df$Days.Until.First.failure/7

Using survival package

df2 <- df[,c(8,16:17)]

#if the SHUNT DID NOT FAIL WITHIN ONE YEAR, ITS TIME = 52
df2$weeks_fail[df2$weeks_fail > 52] <- 52
df2$weeks_fail[is.na(df2$weeks_fail)] <- 52

ggsurvplot(fit1, legend = c(0.2,0.2), 
           legend.title = "Shunt Placement",
           legend.labs = c("0-40 weeks GA", "40+ weeks GA"), title = "Kaplan-Meier Survival Curves for Time to \nFirst Shunt Failure", xlab = "Weeks Since Shunt Implant", risk.table = TRUE, linetype = c("dotted", "solid"), color = c("black"), tables.theme = theme_cleantable())

Warning: Now, to change color palette, use the argument palette= 'black' instead of color = 'black'

df <- read.csv("shunt_figures_data.csv", header = TRUE)

#yes = 1, no = 0
df$Failure.within.first.year.after.surgery <- ifelse(df$Failure.within.first.year.after.surgery=='y', 1, 0)

df$Gestational.Age.at.First.Shunt..in.Days.<- as.numeric(df$Gestational.Age.at.First.Shunt..in.Days.)
df$GA_S <- df$Gestational.Age.at.First.Shunt..in.Days./7  

#less than 40 = 0
#greater than 40 = 1
df$GAlessthan40 <- ifelse(df$GA_S<40,0,1)

FIGURE 2 40 WEEK VISUAL

side by side 2 group bar plot

df$weeks_fail<- df$Days.Until.First.failure/7
df$days_failure <- df$Days.Until.First.failure

df$GA_S_cat <- cut(df$GA_S,
              breaks=c(0, 29.99, 39.99, 49.99, 59.99, 69.99, 500),
              labels=c('20-29', '30-39', '40-49', '50-59', '60-69','70+'))

df %>% 
  ggplot(aes(GA_S_cat)) + 
  geom_bar(aes(fill = as.factor(Failure.within.first.year.after.surgery)), position = position_dodge(width=0.6), width = 0.6, alpha=.6, color="black") +
  ylim(0,30) + 
  ggtitle("Gestational Age at Surgery vs Shunt Failure") +
  ylab("Number of shunt failures") + 
  xlab("Gestational Age at Time of Surgery (weeks)") +
  scale_fill_manual(name = "Shunt Status \nat 1 Year", labels = c("No Failure", "Failure"), values=c("gray80",
                             "gray5")) + theme_bw() + gghisto + theme(legend.position = c(0.85, .8))