Looping through data frames and plotting graphs

Question

I'm working in RStudio, trying to produce some simple graphs and correlations. This is probably a super simple fix but I can't seem to loop through my files and produce plots. See below for files, loop, and sample data frame

> ls()
 [1] "let-7b-5p"     "let_7a_5p"     "miR_125b_5p"   "miR_16_5p"    "miR_182_5p"    "miR_21_5p"    "miR_30e_5p"    "miR_320c_2_3p" "miR_92a_1_3p"  "miR_92b_3p"
[10]  "rRNA-45S"      "tRNA_3p_1"    "tRNA_5p_2"    
> files <- ls()
> for(i in files){
+   plt <- ggplot(`i`, aes_string(x="Five", y = "Three")) +
+       geom_point(shape=16) +
+       geom_smooth(method=lm) 
+   print(plt)
+   pearson <- cor.test(`i`$Five, `i`[, "Three"], method = "pearson", conf.level = 0.95)
+   print(pearson)
+ }
Error: `data` must be a data frame, or other object coercible by `fortify()`, not a character vector
> print(`let-7b-5p`)
       Five        Three       One
A      14.06       13.14       13.62
B      14.45       14.64       14.21
C       7.84       10.23        8.05
D      12.84       13.13       13.07
E      16.55       15.97       16.01
F      12.92       12.02       12.37

I understand that it's seeing "files" as a character vector, but I'm not sure why that's a problem when passed to the loop.

You want to use ls(), which is a character vector with object names, to make your charts? If so, you have yo parse your ls() object into eval and parse. e.g. with the first object: eval(parse(text = ls()[1])) — patL
– patL, Commented Feb 4, 2019 at 15:11
I don't need to use ls(), but I've already imported my files (with a separate loop) and I need a way to list them to pass to the graphing loop. — Stewart Russell
– Stewart Russell, Commented Feb 4, 2019 at 15:18
In your example, files is ls(). Do class(files[1]) for example and check what it returns you. "let-7b-5p" is different from ` let-7b-5p ` — patL
– patL, Commented Feb 4, 2019 at 15:27

zack · Accepted Answer · 2019-02-04 16:00:16Z

1

Passing a string as a character vector when a function (ggplot here) wants a data.frame won't work in the loop for the same reason it won't work out of the loop...R doesn't know to retrieve the object given the name from the global environment.

I would suggest (similar to @patL's comment) retrieving the object and then running the loop:

for(i in files){
  dat <- get(i) # new line
  plt <- ggplot(dat, aes_string(x="Five", y = "Three")) + 
  ...
}

It should be noted that ls() will return a character vector of all objects in the environment, regardless of their class, so if you have anything else defined, you may run into issues there. From the looks of it you may be able to use the pattern argument to ls() to ensure you at least return a vector of object names matching specific patterns.

answered Feb 4, 2019 at 16:00

zack

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1 Comment

Stewart Russell Over a year ago

Adding get(i) did the trick, I now understand the error. Thanks!

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