Output.Rmd

---
title: "Generating output files"
author: "Leo Lahti, Sudarshan Shetty et al."
bibliography: 
- bibliography.bib
output:
  BiocStyle::html_document:
    number_sections: no
    toc: yes
    toc_depth: 4
    toc_float: true
    self_contained: true
    thumbnails: true
    lightbox: true
    gallery: true
    use_bookdown: false
    highlight: haddock 

---
<!--
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteIndexEntry{microbiome tutorial - output}
  %\usepackage[utf8]{inputenc}
  %\VignetteEncoding{UTF-8}  
-->


## Writing diversity table into file

```{r diversity-example4, warning=FALSE, eval = FALSE}
output.dir <- "./"
write.table(div.table, file = "DiversityTable.tab", sep = "\t")
```

## Save clustering image to a file

Save in PDF:

```{r clustering-saving, message=FALSE, warning=FALSE, eval=FALSE}
pdf("myplot.pdf", width = 7, height = 7 * length(hc$order)/20)
plot(hc, hang=-1, main = "Hierarchical clustering")
dev.off()
```

Save in TIFF:

```{r clustering-saving2, message=FALSE, warning=FALSE, eval=FALSE}
tiff("myplot.tif", width = 480, height = 480 * length(hc$order)/20)
plot(hc, hang=-1, main = "Hierarchical clustering")
dev.off()
```

To save in Microsoft EMF format, try the following. If you find a
way to tune figure width for emf files kindly let the admins know.

```{r clustering-saving3, message=FALSE, warning=FALSE, eval=FALSE}
plot(hc, hang=-1, main = "Hierarchical clustering")
savePlot("myplot.emf", type = "emf")
dev.off()
```