---
title: "Prognostic Performance"
author: "Pranjal"
date: "2/21/2019"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Initial Setup and Package Loads in R 

Packages used for the analysis.
```{r initial_setup, cache=FALSE, message = FALSE, warning = FALSE}
library(glmnet);library(survival);library(survminer);library(readxl);library(ggplot2); library(GGally)
library(knitr); library(rmdformats); library(magrittr)
library(skimr); library(Hmisc); library(Epi); library(vcd)
library(tidyverse) 

source("Love-boost.R")

## Global options

options(max.print="75")
opts_chunk$set(comment=NA,
               message=FALSE,
               warning=FALSE)
opts_knit$set(width=75)


skimr::skim_with(numeric = list(hist = NULL),
                 integer = list(hist = NULL))
```

## Loading the Raw Data into R 

Loading raw dataset into R.

Training Data from CCF with minimum and max. survival time.
```{r}
train <- read.csv("dataset_train.csv")
train$censor <- ifelse(train$status == 1,'Censor','Dead')
```

```{r}
ggbarplot(train, x = "Cases", y = "RRS",
          fill = "censor",               # change fill color by cyl
          color = FALSE,            # Set bar border colors to white
          palette = "jco",            # jco journal color palett.
          sort.val = "desc",          # Sort the value in dscending order
          sort.by.groups = FALSE,     # Don't sort inside each group
     #     x.text.angle = 90           # Rotate vertically x axis texts
          )
```

# TCGA DATASET
```{r train_set}
TCGA <- read.csv("dataset_nsclc.csv")
TCGA$censor <- ifelse(TCGA$status == 1,'Censor','Dead')
```

```{r}
ggbarplot(TCGA, x = "Cases", y = "RRS",
          fill = "censor",               # change fill color by cyl
          color = FALSE,            # Set bar border colors to white
          palette = "jco",            # jco journal color palett.
          sort.val = "desc",          # Sort the value in dscending order
          sort.by.groups = FALSE,     # Don't sort inside each group
     #     x.text.angle = 90           # Rotate vertically x axis texts
          )
```


# UPENN DATASET
```{r }
UPENN <- read.csv("dataset_upenn.csv")
UPENN$censor <- ifelse(UPENN$status == 1,'Censor','Dead')
```


```{r}
ggbarplot(UPENN, x = "Cases", y = "RRS",
          fill = "censor",               # change fill color by cyl
          color = FALSE,            # Set bar border colors to white
          palette = "jco",            # jco journal color palett.
          sort.val = "desc",          # Sort the value in dscending order
          sort.by.groups = FALSE,     # Don't sort inside each group
     #     x.text.angle = 90           # Rotate vertically x axis texts
          )
```
