Graphics for Communication

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03

# Graphics for Communication

## R Markdown for Pharma

### Alison Hill &#183; RStudio

#### [rmd4pharma.netlify.app/](https://rmd4pharma.netlify.app/)

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#

# Go here and log in (free):

<https://rstd.io/rmd4pharma-cloud>

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<div class="my-footer">https://rmd4pharma.netlify.app/</div>

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exclude: true

at this point, we should be within a bookdown with html and word doc output options?

Or an rticles with bookdown under the hood?

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.pull-left[

![](https://raw.githubusercontent.com/rstudio/hex-stickers/master/PNG/ggplot2.png)

]

.pull-right[

[`ggplot2` package](https://ggplot2.tidyverse.org/)

[`ggplot2` cheatsheet](https://github.com/rstudio/cheatsheets/blob/master/data-visualization-2.1.pdf)

[R4DS chapter](https://r4ds.had.co.nz/data-visualisation.html)

]

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1

# Get figures in

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# Your turn: Part 1 of 2

**WARM-UP**: open `03-draft.Rmd` and read the source file. It has several figures coded using the `ggplot2` package.

1. Knit the document to the `bookdown::html_document2` format &mdash; behold!

1. Add output options to this format to use one of the [bootswatch themes](https://rmarkdown.rstudio.com/docs/reference/html_document.html) and include a [floating table of contents](https://rmarkdown.rstudio.com/docs/reference/html_document.html#floating-table-of-contents). *(hint: `?html_document`)*

1. Knit to `bookdown::word_document2` (no options)- how does it look?

1. Add `distill::distill_article` as an output format (consider adding a TOC too) and knit- what differences do you see between this and the `bookdown::html_document2` format?

_psst...next slide has answers..._

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# Answer

.pull-left[
```yaml
---
output:
  bookdown::html_document2:
    theme: flatly
    toc: true
    toc_float: true
  bookdown::word_document2: default
  distill::distill_article:
    toc: true
---
```
]

.pull-right[
````
```{r setup, include=FALSE}
knitr::opts_chunk$set(
  echo = FALSE,
  warning = FALSE,
  message = FALSE,
  comment = NA,
  R.options = list(width = 70)
)
```
````

Distill is much less chatty than other outputs due to default `knitr` code chunk options: https://rstudio.github.io/distill/basics.html#code-blocks

]

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# The line-up

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# Including plots

.pull-left[

```r
# PLOT: Age distribution -------------------------------------------------------
ggplot(mockdata, aes(age)) +
  geom_histogram(color = 'white',
                 fill = scico(1, 
                              begin = .3, 
                              palette = "berlin"),
                 bins = 20) +
  labs(x = "Age", 
       y = "Count") +
  scale_y_continuous(
    breaks = scales::pretty_breaks()
  )
```

Will this print?

]

.pull-right[
![](03-graphics_files/figure-html/unnamed-chunk-5-1.png)

]

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# Including plots

.pull-left[

```r
# PLOT: Age distribution -------------------------------------------------------
age_histogram <- 
 ggplot(mockdata, aes(age)) +
 geom_histogram(color = 'white',
 fill = scico(1, 
 begin = .3, 
 palette = "berlin"),
 bins = 20) +
 labs(x = "Age", 
 y = "Count") +
 scale_y_continuous(
 breaks = scales::pretty_breaks()
 )
```

What about this?

]

.pull-right[

]

---

# Including plots

.pull-left[

]

.pull-right[
![](03-graphics_files/figure-html/unnamed-chunk-7-1.png)

]

???

so, how did we get a figure into R Markdown?

Answer: it has to print!

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2

# Chunk options for plots

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# Chunk options for plots

- fig resolution
- fig size
- [fig "device"](https://r4ds.had.co.nz/graphics-for-communication.html#other-important-options)

.footnote[https://yihui.name/knitr/options/#plots]

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# Figure resolution

.pull-left[

]

.pull-right[
![](03-graphics_files/figure-html/unnamed-chunk-9-1.png)

]

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# fig.retina

.pull-left[

````
```{r}
age_histogram
```
````

<img src="03-graphics_files/figure-html/unnamed-chunk-10-1.png" width="70%" />
]

.pull-right[

````
```{r fig.retina=3}
age_histogram
```
````

<img src="03-graphics_files/figure-html/unnamed-chunk-11-1.png" width="70%" />
]

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# out.width

.pull-left[

````
```{r fig.retina=3, out.width="70%"}
age_histogram
```
````

<img src="03-graphics_files/figure-html/unnamed-chunk-12-1.png" width="70%" />
]

.pull-right[

````
```{r fig.retina=3, out.width="10%"}
age_histogram
```
````