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Embed NGCHM into HTML with Knitr

This vignette demonstrates how to construct and embed a simple NG-CHM into R Markdown, then generates a report with knitr. The following sections are below:

Creating an R Markdown file

Creating report with R Markdown starts with a .Rmd file that contains a combination of formatted text and R code chunks. The .Rmd file is fed to knitr, which executes all the R code chunks and create .md document which includes the R code and its output. The markdown file generated by knitr is then processed by pandoc which is used for creating a finished webpage.


---
output:
  html_document:
    toc: true
    toc_float: true
    toc_collapsed: false
    toc_depth: 2
    number_sections: true
    theme:  cerulean
    smooth_scroll: true
params:
  title:  Embedded NGCHM
  author: MD Anderson Cancer Center, Houston, TX
plot: NA
---


````{r setup, include=FALSE}
    knitr::opts_chunk$set(echo = FALSE,fig.align="center")
````
## R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.

When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document.

Creating a NG-CHM

This vignette uses an additional package of demo data, NGCHMDemoData , which can be installed from GitHub with remotes :

The NG-CHM is exported as a stand-alone HTML file with the chmExportToHTML() funciton. The first argument is the NG-CHM created above with chmNew command. The second argument is the desired filename, and the third is a boolean dictating if any existing file of that name should be overwritten.

````{r, echo = FALSE,warning=FALSE, fig.width=20, fig.height=16,fig.align="center", message=FALSE, warning=FALSE}

    remotes::install_github('MD-Anderson-Bioinformatics/NGCHMDemoData', ref='main')
    library(NGCHMDemoData)
    library(NGCHM)
    library(NGCHMSupportFiles)
    hm <- chmNew('tcga-gbm', TCGA.GBM.ExpressionData)
    dataPath=paste(getwd(),'/tcga-gbm.html',sep="")
    chmExportToHTML(hm,dataPath,overwrite=TRUE)
````

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Embedding to R Markdown

htmltools is an R package designed to generate HTML tags from R, we will use htmltools to include generated NGCHM html file as an iframe.

````{r}
    library("htmltools")
    htmltools::includeHTML(dataPath)
````

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Generating report with knitr

RStudio includes a Kint button that enables the readering of .Rmd and preview it with a single click. From R Studio, just click on Knit button to generate HTML file.

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