for loop not creating multiple ggplot objects

Question

I'm hoping to create a ggplot function which loops through a list of objects, and creates individual ggplot objects. The code below successfully prints out the last plot in the list, but nothing is saved as an object.

Thanks in advance for any assistance!

negbinom_list <- c("cytoxic_CD4_CD8.wt.negbinom", "helper_CD4.wt.negbinom")


VolPlot <- function(data, title){

highlight_df <- data %>% filter(p_val_adj<=0.05) %>% filter(avg_logFC<=-0.5 | avg_logFC>=0.5)
data$ID <- row.names(data)
label_df <- filter(data, ID %in% GOI)
data$ID <- row.names(data)
VolPlot_name <- paste( 'volplot', title, sep = '.' )
VolPlot_name <- ggplot(data=data, 
            aes(x=avg_logFC, y =-log10(p_val_adj))) +
  geom_point(alpha=0.4, size=1.75) +
  xlim(c(-2, 2)) +
  xlab("log2 fold change") + ylab("-log10 adjusted p value") +
  theme_bw() +
  theme(legend.position="none") +
  geom_point(data=highlight_df, aes(x=avg_logFC, y =-log10(p_val_adj)), color='red', alpha=0.4,size=1.75) +
  geom_text(aes(label=ifelse(avg_logFC<=-0.75 | avg_logFC>=0.75,as.character(ID),'')),hjust=0,vjust=0) +
  geom_label_repel(data = label_df, aes(label = ID), nudge_y = 36, nudge_x = 1, direction = "x")
}
for(i in negbinom_list){
  print(VolPlot(get(i), i))
}

Try something like: pdf("myPlot.pdf"); for(i in negbinom_list){print(VolPlot(get(i), i))}; dev.off() — zx8754
– zx8754, Commented Sep 12, 2019 at 9:19
In your function, I think there is a typo: VolPlot_name <- ggplot(data=data — zx8754
– zx8754, Commented Sep 12, 2019 at 9:22
I would add gg_list <- list() and then in your for loop do: gg_list[[i]] <- VolPlot(...) — Cole
– Cole, Commented Sep 12, 2019 at 9:54

M M · Accepted Answer · 2019-09-13 04:26:55Z

2

If you are planning to save each ggplot-object into a variable, it might be a better choice to return each ggplot object in a list at the end of the function with return(list(VolPlot_name)). Returning the object alone ends up with just the data frame inside the list.

In this way, you can create a list outside of your function. While you are looping through your variable negbinom_list, you can add each result into the new list.

Later on, you can access each ggplot-object in the list with g.e. new_list[[1]], etc.

Let me know whether it worked for you.

negbinom_list <- c("cytoxic_CD4_CD8.wt.negbinom", "helper_CD4.wt.negbinom")


VolPlot <- function(data, title){

highlight_df <- data %>% filter(p_val_adj<=0.05) %>% filter(avg_logFC<=-0.5 | avg_logFC>=0.5)
data$ID <- row.names(data)
label_df <- filter(data, ID %in% GOI)
data$ID <- row.names(data)
VolPlot_name <- paste( 'volplot', title, sep = '.' )
VolPlot_name <- ggplot(data=data, 
            aes(x=avg_logFC, y =-log10(p_val_adj))) +
  geom_point(alpha=0.4, size=1.75) +
  xlim(c(-2, 2)) +
  xlab("log2 fold change") + ylab("-log10 adjusted p value") +
  theme_bw() +
  theme(legend.position="none") +
  geom_point(data=highlight_df, aes(x=avg_logFC, y =-log10(p_val_adj)), color='red', alpha=0.4,size=1.75) +
  geom_text(aes(label=ifelse(avg_logFC<=-0.75 | avg_logFC>=0.75,as.character(ID),'')),hjust=0,vjust=0) +
  geom_label_repel(data = label_df, aes(label = ID), nudge_y = 36, nudge_x = 1, direction = "x")

return(list(VolPlot_name))
}

list_plots <- list()
count = 1
for(i in negbinom_list){
  list_plots[count] <- VolPlot(get(i), i)
  count = count + 1
}

edited Sep 13, 2019 at 4:26

answered Sep 12, 2019 at 11:33

M M

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4 Comments

Gordon Beattie Over a year ago

Thanks for the response MM! Unfortunately not quite there yet. I ran your code with the following change (due to an unexpected “)”) list_plots[count] <- VolPlot(get(i), i) Got these warnings: Warning messages: 1: In list_plots[count] <- VolPlot(get(i), i) : number of items to replace is not a multiple of replacement length 2: In list_plots[count] <- VolPlot(get(i), i) : number of items to replace is not a multiple of replacement length And creation of “list_plots” in my environment, which contained two data frames

Gordon Beattie Over a year ago

I'm guessing those two data frames in list_plots should be plots, or maybe I'm not extracting them the correct way, plot(list_plots[[2]]) for example, returns plot's interpretation of the data frame

M M Over a year ago

When I return the ggplot-objects as a list, too, it seems to solve the problem. I have changed the code above to solve the error message. Let me know whether it worked for you.

Gordon Beattie Over a year ago

Thats working great now, thanks so much for the assistance! Helps with my understanding of loops in r also.

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