tutorial_knitr_version3.rmd

---
output:
  knitrBootstrap::bootstrap_document:
    title: "Rmarkdown_for_Journal_club"
    theme: amelia
    highlight: sunburst
    theme.chooser: TRUE
    highlight.chooser: TRUE
---

library(knitr)
library(markdown)
knit('tutorial_knitr_version3.rmd')
markdownToHTML("tutorial_knitr_version3.md", "tutorial_knitr_version3.html",fragment.only = TRUE)


This is an R Markdown document, which present the basis element to work with the knitr package in the goal to create some reports.
Here, we presente a collection of tricks to work with knitr in R studio server.


# Why use knitR?

- Generate Report in HMTL, PDF, DOC
- more easier that latex
- integrate in R studio
- combine all elements : documentation, code, result...
- includes Figure, table, summaries :
- allows many operation such as loops
- use Rmarkdown language

# Rmarkdown 
- like HTML but without HTML tag
- include R code.


# Rmarkdown commands.


![alt text](figure/Rmarkdown_command.png)


# Create a new Rmarkdown document.


![alt text](figure/Rmarkdown_doc.png)

# include a R code in Rmarkdown document
- the R code is executed in a chunk
- the variable are global
- the Rmarkdown could have many options (or not).

## Chunk options
Many options are available to control the R code execution

![alt text](figure/chunk.svg)


## Three ways to include a table

### With ktable

```{r results='asis'}
# create a data.frame structure.
library(knitr)
mydata = data.frame(value1= 1:4, value2= 6:9)
rownames(mydata) <- paste("gene", 1:4)
kable(mydata, include.rownames=TRUE)
```

### With googlevis
```{r results='asis'}
library(googleVis)
mydata = data.frame(value1= 1:100, value2= 6:105)
rownames(mydata) <- paste("gene", 1:100)

table = gvisTable(mydata,options=list(page='enable', height='automatic', width='automatic'))
table
```

### With DT package 

```{r results='asis'}
library(DT)

table = datatable(mydata, class = 'cell-border stripe')

table
```


## include a plot.

2 strategies to do that:

### from a R code directly:

Here, we precise no option for the R chunk

```{r}
mydata =rnorm(1000)
plot(mydata, cex= 0.4)
```

In this case, we precise several options in the features of the plot

```{r, fig.height= 14, fig.width= 14, fig.align='center'}
mydata =rnorm(1000)
plot(mydata, cex= 0.4, col= "red")
```


### from a file:

R code to generate the plot
```{r}
png("figure/plot2insert.png")
plot(mydata, cex= 0.4, col= "blue")
dev.off()
```

Include the plot with the markdown syntax.
![alt text](figure/plot2insert.png)


# Strategie with big Data or big Computation:

1. In the case, where you have a large dataset to analyze, it's important to review the 

## Conclusion : 
 - Easy to use
 - One document for Script, documentation, result, reproducible.
 - allows the interactive documentation 


## To go further:

 - CSS style
 - Rpres
 - include loops and template.