CODEWITHSUNDEEP
rggplot2r-markdown
Carmen Sandoval
Carmen Sandoval

Reputation: 2356

Printing figures side by side in R markdown HTML file?

I'm printing two plots with ggplot into an R Markdown HTML output, but I'd like them to appear side by side. Is this possible? Could I set the size of the figures as well?

SO far I can only print them one after the other. I also tried the multiplot function from the R Cookbook, but that severely distorts the plots...

Thanks!

title: "HT Chip MiSeq/HiSeq Analysis"
date: "October 1, 2015"
output: 
  html_document: 
    highlight: haddock
    theme: flatly
---


```{r plots, echo=FALSE}
    genesDetectedDensity_MiSeq <- ggplot(meta.miseq) + geom_density(aes(genesDetected, fill=column, color=seqRun), alpha=0.2) + scale_x_continuous(limits=c(0,2000), breaks=seq(0, 2000, 100)) + ggtitle("Genes Detected across cells from MiSeq Runs")
    return(genesDetectedDensity_MiSeq)

genesDetectedHistogram_MiSeq <- ggplot(meta.miseq) + geom_bar(aes(genesDetected, fill=column, color=seqRun), position="dodge", binwidth=50, alpha=0.2) + scale_x_continuous(limits=c(0,2000), breaks=seq(0, 2000, 100)) + ggtitle("Genes Detected across cells from MiSeq Runs")
return(genesDetectedHistogram_MiSeq)
```

This produces the following:

enter image description here

UPDATE: Following the suggestion I received below, I tried using the gridExtra library, and printed the plots by adding:

grid.arrange(genesDetectedDensity_MiSeq, genesDetectedHistogram_MiSeq, ncol=2)

This almost works, but it's still kind of messy:

enter image description here

Upvotes: 17

Views: 24815

Answers (4)

sbha
sbha

Reputation: 10432

Another simple and straightforward option is using the patchwork package. From the docs:

library(patchwork)
library(ggplot2)

p1 <- ggplot(mtcars) + 
  geom_point(aes(mpg, disp)) + 
  ggtitle('Plot 1')

p2 <- ggplot(mtcars) + 
  geom_boxplot(aes(gear, disp, group = gear)) + 
  ggtitle('Plot 2')

# for side by side:
p1 + p2

# or to stack the plots:
p1 / p2

Upvotes: 3

tjebo
tjebo

Reputation: 23807

You can also change the out.width to <=50% in the chunk options.

Need to have echo = FALSE in the chunk options!

---
title: "Side by Side"
output: html_document
---


You can also change the figure output options. 

```{r base plot, warning = FALSE, echo=FALSE, out.width="50%"}

plot(pressure, main = paste("Lorem Ipsum ",
                        "Ipsum lorem ipsum. ",
                        "\nLorem ipsum", sep=""))

plot(pressure, main = paste("Lorem Two ",
                        "Ipsum lorem ipsum. ",
                        "\nLorem ipsum", sep=""))
```

or, with ggplot objects

```{r ggplot2, warning = FALSE, echo=FALSE, out.width="50%"}
library(ggplot2)
ggplot(pressure, aes(temperature, pressure)) +
  geom_point() +
  ggtitle("plot1")

ggplot(pressure, aes(temperature, pressure)) +
  geom_point() +
  ggtitle("plot2")
```

result

enter image description here

Upvotes: 6

Bg1850
Bg1850

Reputation: 3092

You can use grid.arrange() in the gridExtra library to achieve this :)

Edit : using iris see the image : 

library(gridExtra)

 plot1 <- qplot(iris$Sepal.Length)
 plot2 <- qplot(iris$Sepal.Width)

 grid.arrange(plot1, plot2, ncol=2)

link

Upvotes: 20

ErrantBard
ErrantBard

Reputation: 1501

As long as your using a standard R Markdown html-report you can use the fact that R Markdown uses bootstrap to get two graphs side by side. If you have long titles you can use the escape character \n to line break them, as so:

---
title: "test"
author: "Testperson"
output:
  html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.

When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

<div class = "row">
<div class = "col-md-6">
```{r cars,  warning = FALSE, echo = FALSE, dev=c('svg')}
plot(pressure, main = paste("Lorem Ipsum ",
                        "Ipsum lorem ipsum. ",
                        "\nLorem ipsum", sep=""))
```
</div>
<div class = "col-md-6">
```{r pressure, warning = FALSE, echo=FALSE, dev=c('svg')}
plot(pressure, main = paste("Lorem Ipsum ",
                        "Ipsum lorem ipsum. ",
                        "\nLorem ipsum", sep=""))
```
</div>
</div>

Upvotes: 15

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