Assign a value to a variable within a loop in R

Question

I need to loop over files and then create for each file an object:

Here is an example :

filenames <- Sys.glob("/Users/Desktop/*.nwk")
for (i in filenames ) {
  print(paste0("Processing the phylogeny: ",i))
    p <- a code that generate a figure 
}

And then I generate 5 figures that I call with this code :

multiplot(p1,p2,p3,p4,p5 ncol=2, labels=c('A', 'B','C','D','E'))

But I wondered how can I call assign the 1,2 etc values into the variable objects p?

I tried to create a nb=1 object and then assign as p+nb <- a code that generate a figure, but it does not work

zx8754 · Accepted Answer · 2021-01-13 09:11:46Z

2

There are dedicated packages for plotting/merging multiple plots. patchwork, cowplot, grid, egg, etc.

Use lapply to generate ggplot objects in a list, then use cowplot::plot_grid, something like:

cowplot::plot_grid(
  plotlist = lapply(list.files(...), function(i){
    #import file
    d <- read.table(i)
    #plot
    ggplot(d, aes(...)) + geom_...
  }),
  ncol = 2)

answered Jan 13, 2021 at 9:11

zx8754

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Comments

Ronak Shah · Accepted Answer · 2021-01-13 08:57:02Z

1

You can do that but I'll suggest not to create 5 plot objects in global environment. Store the output of plots in a list.

list_plot <- vector('list', length(filenames))

for (i in seq_along(filenames)) {
  cat("\nProcessing the phylogeny: ",filenames[i])
  list_plot[[i]] <- a code that generate a figure using filenames[i] to read file
}

do.call(multiplot, c(list_plot, ncol=2, labels=c('A', 'B','C','D','E')))

answered Jan 13, 2021 at 8:57

Ronak Shah

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Comments

Grendel · Accepted Answer · 2021-01-13 08:58:04Z

-1

I found a way by doing :

Phylo_name<-paste0("p",nb,sep="")
  eval(call("<-", as.name(Phylo_name), ggtree(tr = phylo,
                                              mapping = aes(color = group)) + geom_tiplab() + theme(legend.position="right")+ 
              scale_color_manual(values=color_vector)))

answered Jan 13, 2021 at 8:58

Grendel

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1 Comment

MrFlick Over a year ago

You are much better off using assign() rather than this eval(call("<-"), ....) setup. But even better don't create a bunch of loose variables in your global namespace. You can easily stick all these values in a list with lapply or purrr::map. I'm not sure which multiplot() function you are using but it probably has a parameter that takes a list of plots.

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