R: Saving Ggplot2 Plots in a List

How to save several plots from an own function into a list in R?

Although I couldn't find the way to save the plots into an object, I found a way to create a presentation with those images thanks to this post and the export package.

library(export) 

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))  
      
      plot(x,y, main=paste0("Plot of ", gene))
      
      hist(x, main=paste0("Plot of ", gene))
      graph2ppt(file="plots.pptx", width=6, height=5,append=TRUE)    } }

myfunction(x=c(1,5,6,2,4),y=c(6,10,53,1,5))

Of course, the width and height of the plots can be changed or put them as a parameter in the function.

Since the package is not available in CRAN for my current R version (4.1.2), I downloaded it from GitHub:
devtools::install_github("tomwenseleers/export")

In addition, I have found another package that I can use for the same purpose (although it adds one extra slide at the beginning, I don't know why)

library(eoffice)

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))  
      
      plot(x,y, main=paste0("Plot of ", gene))
      
      hist(x, main=paste0("Plot of ", gene))
      topptx(file="plots.pptx", width=6, height=5,append=TRUE) 
  }
}

myfunction(x=c(1,5,6,2,4),y=c(6,10,53,1,5))

PS: I found the solution to create a presentation --> How to create a presentation in R with several plots obtained by a function?

How do I save or plot from within lists

Use lapply(plotlist, ggplot2::ggplotGrob) to generate a list of ggplot2 grobs. This list of grobs can then be passed to gridExtra::grid.arrange.

For example:

library(ggplot2)
library(gridExtra)

plotlist <- list()

for(a in c(1:4)) {
    for(b in c(1:4)) {
        plotlist[[paste0("Z",a,b)]] <-
            qplot(rnorm(40,a,b),
                  geom="histogram",
                  xlab=paste0("Z",a,b))
    }
}

grid.arrange(grobs = lapply(plotlist, ggplotGrob), widths = c(1, 1), ncol = 2)

Save a list of plots dynamically

We need to make sure the ggplot object is being passed as the first argument, using the tag argument in the labs() function allows us to assign the plot to a "variable".

imap(.x = combined_mtcars, ~ggplot(.x, aes(x = hp, y = mpg, group = cyl)) +
    geom_line() +
    labs(title = .y, tag="Plot")%>% 
  imap(~ggsave(plot = Plot, file = paste0("/plots/", .y, ".png")))

If that does not work, try this since ggsave may default to the correct plot.

 imap(.x = combined_mtcars, ~ggplot(.x, aes(x = hp, y = mpg, group = cyl)) +
        geom_line() +
        ggtitle(.y)) %>% 
      imap(~ggsave(file = paste0("/plots/", .y, ".png")))

How to store plots in a list when inside a loop?

This answer is based on: Storing plot objects in a list

library(ggplot2)
library(gridExtra)

plist <- list()

for (z in 1:5){
  n <- 100
  k <- seq(0, to=4500+z*2000, length=n)
  tmp <- numeric(n)
  for (i in 1:n){
    tmp[i] <- (5*(i*3)^2)}

  data <- data.frame(n, k, tmp)

  plist[[z]] <- ggplot(data = data) + #data needs to be given!!
    geom_line(aes(x = k, y = tmp)) +
    theme_bw()

  pdf(sprintf("p%s.pdf", z),
      width = 6, height = 4, onefile = T)
  plot(plist[[z]])
  dev.off()
}

do.call(grid.arrange, c(plist, ncol = 5))

Bug in R or am I doing the ggplot saving to a list wrong?

The problem is that the list contains ggplot where the x-aesthetics depend on the i variable. To be more precise, after you run your code i is set to 3. In particular, the x-aesthetics always shows factor(mtcars[, 3]).

You can verify this by trying the following:

print(plots[[1]]) # prints the third plot
i <- 1
print(plots([[1]]) # prints the first plot because now i = 1

Here is an alternative workflow you can try:

plot_cars <- mtcars %>%
  gather(type, val, -mpg) %>%
  nest(data = c(val, mpg)) %>%
  mutate(plot = map(data, ~ggplot(.x,
    aes(x = val, y = mpg)) + geom_point()))

plot_cars$plot[[1]]

Saving a list of plots by their names()

probably you need to pass the names of list:

lapply(names(plots), 
  function(x)ggsave(filename=paste(x,".jpeg",sep=""), plot=plots[[x]]))

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