topic Re: R integration, issue with R Submit File in Discussions

R integration, issue with R Submit File

paul_vanoppen — Thu, 08 Jun 2023 16:44:08 GMT

Hi,

Update: I found a workaround which I posted in the comments.

This JSL script runs without any problems (I am using JMP 16.0.0 (512257) under Windows 10 Pro 64 bit) and generates the expected png output from ggplot in JMP:

LoadExprs = Expr(
	InitR = Expr(
		R Init();
		
		R Submit( "
			library(dplyr)
			library(ggplot2)
			library(palmerpenguins)
		" );
	);
	
	MakePlot = Expr(
		R Submit(
			Eval Insert(
				"\[
				ggplot(data = penguins, aes(x = bill_length_mm, y = flipper_length_mm, colour = species)) +
				geom_point() +
				facet_wrap(. ~ island, nrow = 3)
			]\
			"
			);
		);
		
	);
	
	CapturePlot = Expr(
		JMP_plot = R Get Graphics( png );
		New Window( "Imported Plot", Picture Box( JMP_Plot ) );
	);
	
	RunClose = Expr(
		R Term(); //Close r connection
	);
);
LoadExprs;
InitR;
MakePlot;
CapturePlot;
RunClose;

If I try to call the R script directly, with the exact same R code, it fails with the error message "Get data for ''png" failed".

Here's the JSL script:

LoadExprs = Expr(
	InitR = Expr(
		R Init();
	);

	RunR = Expr(
		R Submit File( "C:\Users\xxx\R_projects\JMP\R_JPM_integration_1.R" );
	);
	
	CapturePlot = Expr(
		JMP_plot = R Get Graphics( png );
		New Window( "Imported Plot", Picture Box( JMP_Plot ) );
	);
		
	RunClose = Expr(
		R Term(); //Close r connection
	);
);
LoadExprs;
InitR;
RunR;
CapturePlot;
RunClose;

This simplified JSL script, my first attempt, also fails with the same error code:

R Init();
R Submit File( "C:\Users\xxx\R_projects\JMP\R_JPM_integration_1.R" );
R Get Graphics( png );
R Term();

And here's the simple R-script I use for this test:

library(dplyr)
library(ggplot2)
library(palmerpenguins)

ggplot(data = penguins, aes(x = bill_length_mm, y = flipper_length_mm, colour = species)) +
  geom_point() +
  facet_wrap(. ~ island, nrow = 3)

Which is identical to the R code in the first script.

Is there a problem with the R Submit File call? What am I missing?

I would prefer to use R Submit File as it saves typing work.

Re: R integration, issue with R Submit File

txnelson — Tue, 10 Jan 2023 05:17:36 GMT

I ran your code under 16.2 and 17.0 running on Windows 10 64bit and got the "Get data for ''png" failed". when running under JMP.

Re: R integration, issue with R Submit File

ih — Tue, 10 Jan 2023 13:33:37 GMT

I think when using R Submit File the plot is not written to the console (I could be wrong, I haven't dug in enough to be sure). I have gotten around this by reading the R file as text into JMP and then submitting it using R Submit.

Re: R integration, issue with R Submit File

paul_vanoppen — Wed, 11 Jan 2023 00:31:29 GMT

Thanks!

Indeed, R Submit works just fine, see code below.

Still, I would like to determine how to make R Submit File work as it prevents having to copy (possibly large) R scripts.

Your assessment of why R Submit File does not work sounds plausible but would require an SAS/JMP expert to confirm.

LoadExprs = Expr(
	InitR = Expr(
		R Init();
	);

	RunR = Expr(
		R Submit ( "
		   library(dplyr)
		   library(ggplot2)
		   library(palmerpenguins)

		   ggplot(data = penguins, aes(x = bill_length_mm, y = flipper_length_mm, colour = species)) +
			  geom_point() +
			  facet_wrap(. ~ island, nrow = 3)
		" );
	);
	
	CapturePlot = Expr(
		JMP_plot = R Get Graphics( png );
		New Window( "Imported Plot", Picture Box( JMP_Plot ) );
	);
		
	RunClose = Expr(
		R Term(); //Close r connection
	);
);
LoadExprs;
InitR;
RunR;
CapturePlot;
RunClose;

Re: R integration, issue with R Submit File

paul_vanoppen — Wed, 11 Jan 2023 00:56:23 GMT

I found a workaround by forcing R to open a graphics window and explicitly plot the graph to that window:

library(dplyr)
library(ggplot2)
library(palmerpenguins)

windows(800,600)
p <- ggplot(data = penguins, aes(x = bill_length_mm, y = flipper_length_mm, colour = species)) +
  geom_point() +
  facet_wrap(. ~ island, nrow = 3)
plot(p)

I now need to worry about plot size but that's acceptable. Here's a screenshot of the script with the JMP graphics window:

Re: R integration, issue with R Submit File

paul_vanoppen — Wed, 11 Jan 2023 01:15:35 GMT

And I do not need the windows() function call either. Just explicitly plotting by calling the plot function is sufficient!

I did find that the JMP error message ("Get data for "png" failed") disappears once I use the windows function call in R. I just end up with an empty window as nothing is explicitly plotted to it.

The code below works fine in conjunction with the JSL scipt using R submit File.

library(dplyr)
library(ggplot2)
library(palmerpenguins)

p <- ggplot(data = penguins, aes(x = bill_length_mm, y = flipper_length_mm, colour = species)) +
  geom_point() +
  facet_wrap(. ~ island, nrow = 3)
plot(p)