How to create a presentation in R with several plots obtained by a function?-CodePudding

I have created one function that gives you the number of plots that you want, depending on a list.

This is the example that I have created.

list_genes <- c("GEN1", "GEN2", "GEN3")


myfunction <- function(x,y){
  
  for(gene in list_genes){
    # This to draw both plots
      par(mfrow=c(2,1))  
      
      stripchart(x, method="jitter", vertical=F, main=paste0("Plot of ", gene))
      
      hist(x, main=paste0("Plot of ", gene))
  }
}

myfunction(x=c(1,5,6,2,4,30,23,12,45))

My final objective is to create a presentation (automatically) with all of the plots that I generate from my function.

However, If I try to create an ioslides_presentation, they don't appear (only the first one and a bit of the second).

---
title: "My presentation"
output: ioslides_presentation
---

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

## PLOTS 

```{r}
list_genes <- c("GEN1", "GEN2", "GEN3")


myfunction <- function(x,y){
  
  for(gene in list_genes){
    # This to draw both plots
      par(mfrow=c(2,1))  
      
      stripchart(x, method="jitter", vertical=F, main=paste0("Plot of ", gene))
      
      hist(x, main=paste0("Plot of ", gene))
  }
}

myfunction(x=c(1,5,6,2,4,30,23,12,45))
```

The code is a small example of my original function but it is enough to show you my problem. I tried to save the plots into objects but since it is base R, I can't (or at least, it doesn't work properly). I know that I could do this with ggplot2 but, I wanted to ask here just in case someone knows how to do make presentations in this case, before changing the complete original function.

Does anyone know how to solve it?

Thanks very much in advance

Regards

CodePudding user response：

There are several ways to get this. The, IMHO easiest is to take the mfrow or mfcol call out of the function and to create a global one for all plots, e.g.:

---
title: "My presentation"
output: ioslides_presentation
---

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

## PLOTS

```{r}
list_genes <- c("GEN1", "GEN2", "GEN3")

myfunction <- function(x,y){
  for(gene in list_genes){
    stripchart(x, method = "jitter", vertical = FALSE, 
               main = paste0("Plot of ", gene))
    hist(x, main = paste0("Plot of ", gene))
  }
}

par(mfcol = c(2, 3))
myfunction(x = c(1, 5, 6, 2, 4, 30, 23, 12, 45))
```

slide with 6 plots

An additional note: It is better to use FALSE and not F in R code. FALSE is a reserved word while F is "fragile" as it can be re-defined.

CodePudding user response：

Thanks to @tpetzoldt and this post, I found exactly what I needed it!

I had to change a bit the function and create the headers of the presentation inside the loop.

Here is the solution:

---
title: "Create a presentation with several plots"
output:
    ioslides_presentation
---

```{r, echo=FALSE}
myfunction <- function(x, gene){
    # This to draw both plots
      par(mfrow=c(2,1))  
      
      stripchart(x, method="jitter", vertical=F, main=paste0("Plot of ", gene))
      
      hist(x, main=paste0("Plot of ", gene))
}
```

```{r, echo=FALSE}
list_genes <- c("GEN1", "GEN2", "GEN3")
```


```{r, echo = FALSE, results = "asis"}
for(gene in list_genes){
  cat("\n\n## Plot of ", gene, "\n\n")
  myfunction(x=c(1,5,6,2,4,30,23,12,45), gene)
}
```