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Question

I am trying to add some chemical structure images to some plots I have created. I am using the ACToR database to access the chemical structures. For example:

( http://actor.epa.gov/actor/image?format=png%3Aw250%2Ch250&casrn=80-05-7 )

The nice thing about this site is you can change the size and the chemical within the url, so I can automate grabbing the images. My hope was to store an object containing CAS numbers, then iterate through the CAS numbers to make the plots.

For example:

library(png)
casnums <- ("80-05-7","77-40-7","1478-61-1")
image.list <- list()
for(cas in casnums){
  image.list[[cas]] <- readPNG(paste0("http://actor.epa.gov/actor/image?format=png%3Aw1000%2Ch1000&casrn=",cas))
}

I have tried using readPNG from the png package, and tried to use the rgdal package as well. Unfortunately, as far as I can tell, ACToR will only generate the images in a png or jpeg format - so I cannot use the grImport package for reading vector images.

I am really hoping to find a solution where I do not have to manually download each image - there are a lot of them. I would be open to a solution where R goes and dowloads the images to a folder, then I could use something like the png package, or the rgdal package to load the image and plot them.

In response to @ialm: Here is what I tried after your first comment:

> download.file(url="http://actor.epa.gov/actor/image?format=png%3Aw250%2Ch250&casrn=80-05-7",destfile="test.png")
trying URL 'http://actor.epa.gov/actor/image?format=png%3Aw250%2Ch250&casrn=80-05-7'
Content type 'image/png' length 200 bytes
opened URL
downloaded 6691 bytes

Warning message:
In download.file(url = "http://actor.epa.gov/actor/image?format=png%3Aw250%2Ch250&casrn=80-05-7",  :
  downloaded length 6691 != reported length 200

When I go to open the image it is only 7 KB and I get the follow message in the image viewer: "Windows Photo Viewer can't open this picture because the file appears to be damaged, corrupted, or is too large."

I should note that I am (against my will) using Windows 7. I also tried using both RStudio, and R. RStudio gave me the warning message, and R did not - but R created what appears to be the same file (7KB) and still does not open.

In response to @Greg Snow: Just to add some context, I ran the following from a fresh R Console in RStudio. I used 64 bit Rv3.0.1 and 64-bit RStudio v0.97.551.

> library(png)
> search()
 [1] ".GlobalEnv"        "package:png"       "tools:rstudio"     "package:stats"     "package:graphics"  "package:grDevices"
 [7] "package:utils"     "package:datasets"  "package:methods"   "Autoloads"         "package:base"     
> con <- url("http://actor.epa.gov/actor/image?format=png%3Aw1000%2Ch1000&casrn=1478-61-1",open='rb')
> rawpng <- readBin(con, what='raw', n=1e6)
> close(con)
> png1 <- readPNG(rawpng)
Error in readPNG(rawpng) : libpng error: bad adaptive filter value
> ls()
[1] "con"    "rawpng"

Answer 1

(Just posting my comment as an answer)

You can use the download.file function to download files from the web.

In addition, Windows users may have to alter some of the arguments. It seems that mode="wb" is a necessary argument to download and view these png files correctly.

So, something like:

download.file("http://actor.epa.gov/actor/image?format=png%3Aw1000%2Ch1000&casr‌​‌​n=80-05-7", 
              destfile="tmp.png", mode="wb")

worked for me.

Answer 2

Here is an approach that worked for me for a single image (it could be wrapped in a function to be used in the loop):

con <- url("http://actor.epa.gov/actor/image?format=png%3Aw1000%2Ch1000&casrn=1478-61-1",
    open='rb')

rawpng <- readBin(con, what='raw', n=50000)

close(con)

png1 <- readPNG(rawpng)

I tested it using:

plot(1:10, type='n')
rasterImage( as.raster(png1), 3,3,8,8 )

It took some guesswork to get the 50000 and that may be different for other files (actually I should have used 48849, but then it really would be likely to change between files).

Answer 3

Please note that the Bioconductor R package EBImage is capable of loading images directly from an URL and visualizing them:

library(EBImage)

img = readImage("path/to/your/image/file or URL")
display(img, method = "raster")

Cheers,

Andrzej