Calling R in perl

blackzero has asked for the wisdom of the Perl Monks concerning the following question:

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Re: Calling R in perl by frozenwithjoy (Priest) on Dec 16, 2012 at 01:12 UTC
I regularly use Statistics::R and it works great. You can put all of your R commands within your Perl script, or if you have a lot of R stuff to run, you can use it to specify variables and then run an entire external R script. The examples on the linked page are clear and helpful. Take a look at them and if you have any more questions, let me know. EDIT: Here is a snippet from one of my Perl scripts which demonstrates setting variables, running R commands from within Perl, and running R scripts from within Perl. The only thing it is really missing is an example of retrieving a value from an R variable (e.g., `$value_returned_from_R = $R->get('some.r.variable')` ): my $R = Statistics::R->new(); $R->set( 'filenames', \@filenames ); $R->set( 'id', $id ); $R->set( 'par1', $par1 ); $R->set( 'par2', $par2 ); $R->run_from_file( "genoplot_by_id.build_df.R" ); $R->run_from_file( "genoplot_by_id.build_plot.R" ); $R->run( qq`setwd("$plot_dir")` ); $R->run( qq`ggsave( filename = paste("$plot_path", "$plot_format", sep = "."), plot = geno.plot, width = $plot_width, height = $plot_height)` ); [download] EDIT #2: A couple more examples... Using an array of R commands or a heredoc with multiple R commands (example taken from Statistics::R): # Array of R commands: my $out1 = $R->run( q`a <- 2`, q`b <- 5`, q`c <- a * b`, q`print("ok")` ); # Here-doc with multiple R commands: my $cmds = <<EOF; a <- 2 b <- 5 c <- a * b print('ok') EOF my $out2 = $R->run($cmds); [download]	[reply] [d/l] [select]
Re^2: Calling R in perl by blackzero (Acolyte) on Dec 16, 2012 at 12:52 UTC
Ok, thank you very much to all for the replies. Statistics::R seens to be what I want. I've installed Statistics::R But I have some issues. My code is this: #!/usr/bin/perl use strict; use warnings; use Statistics::R; my @lines; my $line; my $csv_check = shift @ARGV; #Mark for csv check----- @ARGV = $csv_check; while ( defined( $line = <> ) ) { push @lines, $line; } save_array_output(@lines, ".out"); print "\@lines = \n @lines "; my $R = Statistics::R->new() ; $R->startR ; $R -> send('library(genetics);'); $R -> send('table <- read.table("/home/user/my_path/data_freq.txt.out" +, header=T, row.names=2);'); $R -> send('g1 <- table[, 2];'); $R -> send('meang1 <- mean(g1)'); $R -> send('print(meang1);'); $R -> send('write.table(g1, "/home/user/my_path/g1.txt");'); $R -> send('write.table(meang1, "/home/user/my_path/meang1.txt");'); #my @results1 = get('g1'); print "\@results1 = ", @results1, "\n"; $R->stopR() ; #----------------------------------------------- sub save_array_output { @lines = @_; my $mid_name = pop @lines; my $output_name = $csv_check.$mid_name; open(MYOUTFILE, ">:utf8", $output_name); # Open output file print MYOUTFILE "@lines \n"; close(MYOUTFILE); # Close output file } [download] data_freq.txt is this: `Locus Alleles frequencies Bet01 230 0.166666666666666657415 Bet01 238 0.500000000000000000000 Bet01 244 0.333333333333333314830 Bet05 101 0.285714285714285698425 Bet05 103 0.500000000000000000000 Bet05 105 0.142857142857142849213` [download] I run my program with "./perl-R3.pl data_freq.txt". I am able to call R, activate the genetics package, make it run the file data_freq.txt.out, do the calculations, save the results in "g1.txt" and "meang1.txt". OK. But I cant get back g1 to perl. If I uncomment the line "#my @results1 = get('g1');", I get this error: `Undefined subroutine &main::get called at ./perl-R3.pl line 35.` If I try to pass values from perl to R directly with a command like "$R -> set('table', \@lines);", I also receive an error: `Can't locate object method "set" via package "Statistics::R" at ./perl-R3.pl line ##` Whats the problem here? Also, if I try to set the work directory to R with a command like "$R -> send('setwd("/home/user/my_path/");');", the program hangs.	[reply] [d/l] [select]
Re^3: Calling R in perl by frozenwithjoy (Priest) on Dec 16, 2012 at 18:27 UTC
OK, I think a couple changes will fix everything. First, the method for running a line of R code is `run()`, not `send()`, so change `$R->send(...)` to `$R->run(...)`. (The method `send()` still works, but seems to have been deprecated for a long time. I'd avoid its use in case it is ever completely dropped.) Second, to retrieve values from R, you need to change `my @results1 = get('g1');` to `my $results = $R->get('g1')`. Notice that there are two changes here: (1) the addition of `$R->` and (2) `$results` is an array reference rather than an array. Regarding your problem with `$R->set()`, can you show a few lines of code where you are using it in context? I don't see any obvious problems with what you wrote there. One more thing: you are putting your R commands in single quotes, but the Statistics::R docs recommend quoting with q`...` (if you aren't interpolating Perl variables) or qq`...` (if you are interpolating). Those are backticks, by the way (but, really, any character not used in typical R code should suffice). The reason for this is that if you have single or double quotes in your R commands, you won't run into troubles. Another thing to watch out for is if you are wrapping your R code in double quotes because you need to interpolate Perl variables and are using `$` in your R code to specify a column of data, for example, you need to escape it (e.g., `dataframe\$sample1`). EDIT: I'm trying to understand why you are having issues with `$R->set()`. Are you able to run the following code successfully? Also, I don't think it is causing any errors, but you should remove the spaces between your objects and methods (e.g., change `$R -> set(...)` to `$R->set(...)`) #!/usr/bin/env perl use strict; use warnings; use Statistics::R; my @numbers = ( 1 .. 10 ); my $R = Statistics::R->new(); $R->set( 'x', \@numbers ); $R->run( q`x = x ^ 2` ); my $squares = $R->get('x'); print "@$squares"; __END__ 1 4 9 16 25 36 49 64 81 100 [download]	[reply] [d/l] [select]
Re^4: Calling R in perl by blackzero (Acolyte) on Dec 16, 2012 at 19:26 UTC
Re^5: Calling R in perl by frozenwithjoy (Priest) on Dec 16, 2012 at 19:52 UTC
Some notes below your chosen depth have not been shown here
Re: Calling R in perl by ww (Archbishop) on Dec 15, 2012 at 23:58 UTC
Feed three words of your question to big G, "Perl R Integrate." See the second item in the second list: Putting Perl Back on Top in the Fields of Scientific and Financial Computing Perl Module: The Statistics::useR is intended to integrate statistical power of R and comprehensive power of Perl Amazon book listing: Building Biolinformatics Solutions Perhaps these -- just a few of the items from pages 1 - 10 -- will be helpful.	[reply]
Re: Calling R in perl by davido (Cardinal) on Dec 16, 2012 at 01:06 UTC
Surprisingly, http://search.cpan.org mostly DWIM when I enter the single search term of "R". I was expecting a lot of unrelated clutter, but it seems to work well in this case. Dave	[reply]
Re: Calling R in perl by CountZero (Bishop) on Dec 16, 2012 at 09:27 UTC
I have several Perl scripts that simply write an R-script (hey, it is just text) and then call R through the `system` command or backticks. CountZero A program should be light and agile, its subroutines connected like a string of pearls. The spirit and intent of the program should be retained throughout. There should be neither too little or too much, neither needless loops nor useless variables, neither lack of structure nor overwhelming rigidity." - The Tao of Programming, 4.1 - Geoffrey James My blog: Imperial Deltronics	[reply] [d/l]
Re: Calling R in perl by erix (Prior) on Dec 16, 2012 at 13:08 UTC
Here are some older nodes that may contain useful bits: using R from Perl Passing parameters to R script	[reply]
Re: Calling R in perl by blackzero (Acolyte) on Dec 17, 2012 at 00:58 UTC
Can you help me here? I never really used CPAN, so it may be a silly question. Sorry. But when I try to use it with the command "install Statistics::R" it return the following error: `Failed during this command: FANGLY/Statistics-R-0.30.tar.gz : make_test NO` Any advices about that? NOTE: I'm running a Fedora 17 and perl 4:5.14.3-218.fc17, and I ran cpan with "sudo perl -MCPAN -e shell" EDIT: I tried to install it by hand using the commands "perl Makefile.PL", "make", "make test", "make install". But when I rum "make test". It fails and returns this error message: `Test Summary Report ------------------- t/08-errors.t (Wstat: 256 Tests: 10 Failed: 1) Failed test: 10 Non-zero exit status: 1 Files=9, Tests=10195, 64 wallclock secs ( 8.93 usr 0.48 sys + 54.43 c +usr 4.36 csys = 68.20 CPU) Result: FAIL Failed 1/9 test programs. 1/10195 subtests failed. make: ** [test_dynamic] Erro 1` [download]	[reply] [d/l] [select]
Re^2: Calling R in perl by Anonymous Monk on Dec 17, 2012 at 02:44 UTC
make test TEST_VERBOSE=1	[reply]
Re^3: Calling R in perl by blackzero (Acolyte) on Dec 17, 2012 at 03:10 UTC
TEST_VERBOSE=1 Didn't work The same error keep occurring	[reply]
Re^4: Calling R in perl by Anonymous Monk on Dec 17, 2012 at 11:55 UTC
Re: Calling R in perl by blackzero (Acolyte) on Dec 16, 2012 at 15:43 UTC
Erix, have you saw the problem I replied to frozenwithjoy answer? If you know how to get a object from R back to perl with Statistics::R, can you please send me an example?	[reply]
Re: Calling R in perl by blackzero (Acolyte) on Dec 17, 2012 at 13:24 UTC
OK. Statistics::R seens to be working fine now I just ignores the error message in the test and went ahead with the installation, just as was told me in here: http://www.perlmonks.org/?node_id=1009156 But still I have two problems (that I hope are the last ones). First of all, when I try to pass my table from perl to R with the comand "$R -> set( 'table', \@lines );", it returns this error: `Problem running this R command: g1 <- table[, 3]; Got the error: wrong number of dimmensions` [download] I scaped that creating an output file from perl (named "data_freq.txt.out" and telling R to import from that. But this doesnt seens the right way to do it. Second. When I try to return a table from R to perl, importing it to an array (in "my @results1 = $R->get('g1');"), I would like all the values in the table to be passed to this array (@results1). So I could shift and pop values from that array to use in other perl things (Mostly to create an nice output file) Instead, what I get is an array with a single element that is some kind of octodecimal value (I guess) How can I fix that? Someone already told me to use "$results1" instead of "@results1". But that gives me the same output. Besides, it will create an scalar and that is not what I want NOTE: "my $media = $R->get('meang1');" do work! I guess thats is because its a single value. HERE are my codes, wich I call with "./perl-R4.pl data_freq.txt" perl-R4.pl #!/usr/bin/perl use strict; use warnings; use Statistics::R; my @lines; my $line; my $csv_check = shift @ARGV; #Mark for csv check----- @ARGV = $csv_check; while ( defined( $line = <> ) ) { push @lines, $line; } shift @lines; save_array_output(@lines, ".out"); print "\@lines = \n @lines "; my $R = Statistics::R->new() ; $R->startR ; $R->run('library(genetics);'); $R->run('setwd("/home/user/tests/");'); #$R->set( 'table', \@lines ); $R->run('table <- read.table("/home/user/tests/data_freq.txt.out");'); $R->run('g1 <- table[, 3];'); $R->run('meang1 <- mean(g1)'); $R->run('print(meang1);'); $R->run('write.table(g1, "g1.txt");'); $R->run('write.table(meang1, "meang1.txt");'); my $media = $R->get('meang1'); my $results1 = $R->get('g1'); print "\$results1 = ", $results1, "\n"; print "\$media = ", $media, "\n"; $R->stopR() ; #----------------------------------------------- sub save_array_output { @lines = @_; my $mid_name = pop @lines; my $output_name = $csv_check.$mid_name; open(MYOUTFILE, ">:utf8", $output_name); # Open output file print MYOUTFILE "@lines \n"; close(MYOUTFILE); # Close output file } [download] data_freq.txt Locus Alleles frequencies Bet01 230 0.166666666666666657415 Bet01 238 0.500000000000000000000 Bet01 244 0.333333333333333314830 Bet05 101 0.285714285714285698425 Bet05 103 0.500000000000000000000 Bet05 105 0.142857142857142849213 Bet05 109 0.071428571428571424606 Bet06 138 0.055555555555555552472 Bet06 140 0.111111111111111104943 Bet06 146 0.833333333333333370341 Bet12 108 0.111111111111111104943 Bet12 110 0.055555555555555552472 Bet12 112 0.444444444444444419773 Bet12 114 0.277777777777777790114 Bet12 116 0.055555555555555552472 Bet12 118 0.055555555555555552472 [download]	[reply] [d/l] [select]
Re: Calling R in perl by blackzero (Acolyte) on Dec 18, 2012 at 13:39 UTC
Any tips?	[reply]


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