---
title: "4.5 - Heatmap plots"
output: 
  html_document:
    self_contained: true
    number_sections: no
    theme: flatly
    highlight: tango
    mathjax: null
    toc: true
    toc_float: true
    toc_depth: 2
    css: style.css
  
bibliography: bibliography.bib    
vignette: >
  %\VignetteIndexEntry{"4.5 - Heatmap plots"}
  %\VignetteEngine{knitr::rmarkdown}
  \usepackage[utf8]{inputenc}
---

```{r, echo = FALSE,hide=TRUE, message=FALSE, warning=FALSE}
library(ELMER.data)
library(ELMER)
library(DT)
library(dplyr)
library(BiocStyle)
```
<br>

# Loading required data for plot
```{r,eval=TRUE, message=FALSE, warning = FALSE, results = "hide"}
# Load results from previous sections
mae <- get(load("mae.rda"))
```

# Heatmap 

Generate a heatmap of paired probes.

```{r results='hide', echo=TRUE,eval=F, message=FALSE, warning=FALSE, fig.width=10, fig.height=5, fig.cap="Heatmap of paired pairs."}

pair <- read.csv("result/getPair.hypo.pairs.significant.csv")

heatmapPairs(data = mae, 
             group.col = "definition",
             group1 = "Primary solid Tumor", 
             annotation.col = c("years_smoked","gender"),
             group2 = "Solid Tissue Normal",
             pairs = pair,
             filename =  NULL)

```