example1.Rmd

---
title: "RMarkdown Example"
author: "Simon Cockell"
date: "22/05/2020"
output: html_document
---

```{r load_packages, warning=FALSE, include=FALSE}
library(viridis)
library(readr)
library(knitr)
```

# Heading 1

This is a paragraph of text. Markdown lets us format the text in **bold**, *italics*, as `code` and [links](https://youtube.com).

 * This
 * is
 * a
 * bulleted
 * list

Some more text here.

 1. This
 1. is 
 1. a 
 1. numbered
 1. list
 
Final example: some maths $E = mc^{2}$

```{r figure1, include=TRUE}
image(volcano, col=viridis(200))
```

# Figure 2

Here is an alternative colour scheme.

```{r figure2, fig.cap="Figure 2 - Magma colour scheme", fig.height=10, cache=TRUE}
image(volcano, col=viridis(200, option="A"))
```

## Heading level 2

### Heading level 3

Here is a table example.

```{r table1}
dat = read_tsv('../covid-rnaseq/filtered_nhbe_results.txt')
kable(dat)
```

```{bash bash_eg}
ls -l -h .
```

```{python python_eg}
x = "Hello world"
print(x)
```