fig2_change-in-nlr.Rmd

---
title: "fig2_change-in-nlr"
author: "Dan Spakowicz"
date: "12/21/2018"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)

# CRAN packages
library(magrittr)
library(dplyr)
library(survival)
library(survminer)

```


```{r load data}
s1 <- readRDS("nlr-survival-deident.RDS")

set.seed(12345)
```

## Figure 2

```{r fig 2a}
change.cut <- surv_cutpoint(s1, time = "months", 
                            event = "vitalstatus", 
                            variables = "nlr_change")$cutpoint$cutpoint

s1.cat <- 
  s1 %>%
  mutate(nlr_change_cat = ifelse(nlr_ratio < change.cut, 0, 1))

sfit.cat <-  survfit(Surv(months, vitalstatus) ~ factor(nlr_change_cat), data = s1.cat)

p2a <- ggsurvplot(sfit.cat, conf.int = TRUE, pval = FALSE, ggtheme = theme_bw(), legend = "none")

p2a + ggsave("figures/fig2a_surv_1strat.pdf", height = 4, width = 4)

ggpar(p2a, font.main = c(10))
```


```{r fig 2b}
p2c <- s1 %>%
  ungroup() %>%
  select(nlr_change, vitalstatus, months) %>%
  mutate(alivedead = ifelse(vitalstatus == 1, "dead", "alive")) %>%
  ggplot(aes(x = months, y = nlr_change)) +
  stat_smooth() + 
  # geom_point(alpha = 0.1) +
  # ylim(-1, 1)
  theme_bw() +
  labs(y = "Change in NLR", 
       x = "Months to Last Follow-Up or Death")

p2c +
  ggsave("figures/fig2c_change-in-nlr_vs_time_statsmooth.pdf", height = 4, width = 4)
```

```{r fig 2c}
s3 <- 
  s1 %>%
  select(months, vitalstatus, nlr_baseline, nlr_change) %>%
  mutate("Change in NLR^3" = nlr_change^3) %>%
  rename("Change in NLR" = "nlr_change") %>%
  rename("Baseline NLR" = "nlr_baseline")

cph.m3o3 <- coxph(Surv(months, vitalstatus) ~ `Baseline NLR` + `Change in NLR` + `Change in NLR^3`, data = s3)

ggforest(cph.m3o3) +
  ggsave("figures/fig2d_coxph_cubic-change.pdf", height = 2, width = 8)
```