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In our last post we quickly went over how to create a new R-Markdown document and embed a Plotly graph in it. In this post we’ll get into more details around how to control code output using chunk options.
As shown in our previous post, for the embedded R code to be evaluated, it’ll need to be written inside a code-chunk as shown below.
```{r Code Chunk, chunk options here...}
# R code here...
```
Chunk options
Knitr provides a lot of ways to control the output that shows up in the final document. We’ll highlight a few common ones.
Echo
echo allows control over visibility of the actual R code in a chunk. Set it to FALSE to hide the R code from showing up. Note that the code chunk will still be evaluated and any outputs mirrored in the final document. Use eval = FALSE if you do not need a code chunk to be evaluated at all.
```{r Code Chunk, echo = FALSE}
# R code will be evaluated but not shown in the final HTML document
# Useful when only plots / charts / text output needs to be shown and not the
# code that generated it...
```
Message
Notice how if you use include() in a code chunk, messages from the R console are mirrored in the final document as well? By default, when knitr evaluates a code chunk, it mirrors any messages that show up in the console as well. We can turn that off using message = FALSE.
```{r Code Chunk, message = FALSE}
# R code
# Messages from R-Console will not show up in final document
```
With message = TRUE
library(plotly) ## Loading required package: ggplot2 ## ## Attaching package: 'plotly' ## ## The following object is masked from 'package:ggplot2': ## ## last_plot ## ## The following object is masked from 'package:graphics': ## ## layout
With message = FALSE
library(plotly)
Results
Controls the mirroring of output when a code chunk is evaluated. This includes text output as well as charts / graphs. Four values can be assigned: (see http://yihui.name/knitr/options/ for more details)
markup– markup output using output hookasis– raw outputhold– shows output after all code is evaluatedhide– no output is shown
```{r Code Chunk, results = 'markup'}
# R code will be evaluated but not shown in the final HTML document
# Useful when only plots / charts / text output needs to be shown and not the
# code that generated it...
```
With results = ‘markup’
str(mtcars) ## 'data.frame': 32 obs. of 11 variables: ## $ mpg : num 21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 ... ## $ cyl : num 6 6 4 6 8 6 8 4 4 6 ... ## $ disp: num 160 160 108 258 360 ... ## $ hp : num 110 110 93 110 175 105 245 62 95 123 ... ## $ drat: num 3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 ... ## $ wt : num 2.62 2.88 2.32 3.21 3.44 ... ## $ qsec: num 16.5 17 18.6 19.4 17 ... ## $ vs : num 0 0 1 1 0 1 0 1 1 1 ... ## $ am : num 1 1 1 0 0 0 0 0 0 0 ... ## $ gear: num 4 4 4 3 3 3 3 4 4 4 ... ## $ carb: num 4 4 1 1 2 1 4 2 2 4 ...
With results = ‘asis’
str(mtcars)
‘data.frame’: 32 obs. of 11 variables: $ mpg : num 21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 … $ cyl : num 6 6 4 6 8 6 8 4 4 6 … $ disp: num 160 160 108 258 360 … $ hp : num 110 110 93 110 175 105 245 62 95 123 … $ drat: num 3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 … $ wt : num 2.62 2.88 2.32 3.21 3.44 … $ qsec: num 16.5 17 18.6 19.4 17 … $ vs : num 0 0 1 1 0 1 0 1 1 1 … $ am : num 1 1 1 0 0 0 0 0 0 0 … $ gear: num 4 4 4 3 3 3 3 4 4 4 … $ carb: num 4 4 1 1 2 1 4 2 2 4 …
With results = ‘hide’
str(mtcars)
Figure related options
The set of fig.* options allow control over how charts / graphs are shown in the final document. Below are some examples. For more details see http://yihui.name/knitr/options/
Width and Height
Use fig.width and fig.height. Note that units are in inches by default
Small
```{r Code Chunk, fig.width = 2, fig.height = 2}
df <- diamonds[sample(1:nrow(diamonds), size = 2000),]
plot_ly(df, x = x, y = price, mode = "markers", color = cut, size = z) %>%
layout(title = "Diamonds")
```
BIG
```{r Code Chunk, fig.width = 8, fig.height = 8}
df <- diamonds[sample(1:nrow(diamonds), size = 2000),]
plot_ly(df, x = x, y = price, mode = "markers", color = cut, size = z) %>%
layout(title = "Diamonds")
```
Alignment
Figure alignment for figures using base graphics and or ggplot2 is easy. Simply use fig.align = 'left' / 'right' / 'center'
```{r Code Chunk, fig.align = 'right'}
df <- diamonds[sample(1:nrow(diamonds), size = 2000),]
plot_ly(df, x = x, y = price, mode = "markers", color = cut, size = z) %>%
layout(title = "Diamonds")
```
But for figures generated using the plot_ly() function, we’ll need to use the <div> tag. Use the following as an example.
<div style = "float: right">
```{r Code Chunk}
df <- diamonds[sample(1:nrow(diamonds), size = 2000),]
plot_ly(df, x = x, y = price, mode = "markers", color = cut, size = z) %>%
layout(title = "Diamonds")
```
</div>
IFrame
<iframe> allows Plotly charts available in your Plotly account to be embedded in a R-Markdown document. Simply point the src argument to the chart’s ‘embed’ link as provided by Plotly. See http://help.plot.ly/embed-graphs-in-websites/ for more details.
<iframe width="450" height="400" frameborder="0" scrolling="no" src="https://plot.ly/~riddhiman/47.embed"></iframe>
Note that using <iframe> makes the HTML file more blog friendly.
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