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BINF634 Perl and R

BINF634 Perl and R. Some R References. The R Book by Michael J. Crawley Statistics An Introduction using R by Michael J. Crawley Introductory Statistics with R (Statistics and Computing) by Peter Dalgaard R Graphics , Paul Murrell

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BINF634 Perl and R

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  1. BINF634 Perl and R BINF634 - Perl and R

  2. Some R References • The R Book by Michael J. Crawley • Statistics An Introduction using R by Michael J. Crawley • Introductory Statistics with R (Statistics and Computing) by Peter Dalgaard • R Graphics, Paul Murrell • Data Analysis and Graphics Using R, John Maindonald et al. • Using R for Introductory Statistics by John Verzani BINF634 - Perl and R

  3. Making it Go • Under Unix/LINUX Type R (or the appropriate path on your machine) • Under Windows Double click on the R icon BINF634 - Perl and R

  4. Making it Stop • Type > q() • q()is a function execution • Everything in R is a function • q merely returns a listing of the function BINF634 - Perl and R

  5. R as a Calculator > log2(32) [1] 5 > sqrt(2) [1] 1.414214 > seq(0, 5, length=6) [1] 0 1 2 3 4 5 > plot(sin(seq(0, 2*pi, length=100))) BINF634 - Perl and R

  6. Syntax • Everything that we type in R is an expression • We may have multiple expressions on each line separated by ; 2+3;4*5;6-9 • We use <- or = for making assignments b<-5+9 or b = 5+9 • R commands are case sensitive • The result of any expression is an object BINF634 - Perl and R

  7. Recalling Previous Commands • In WINDOWS/UNIX one may use thearrow up key or thehistory command under the menus • Given the history window then one can copy certain commands or else past them into the console window BINF634 - Perl and R

  8. Getting Help • In both environments we may use help(command name) ?command name > help("ls") > ? ls • We may also use methods(command name) • html-based help help.start() • For commands with multiple methods based on different object types BINF634 - Perl and R

  9. Assignments in R • Some Examples > cat<-45 > dog=66 > cat [1] 45 > dog [1] 66 > 77 -> rat > rat [1] 77 • Note = is used for specifying values in function calls BINF634 - Perl and R

  10. Vectors • A vector example > a<-c(1,2,3,4) > length(a) [1] 4 > a [1] 1 2 3 4 • An example with character strings > name<-c("Jeff","Solka") > name [1] "Jeff" "Solka“ > name[1] [1] "Jeff" BINF634 - Perl and R

  11. Graphics in R • win.graph() or in UNIX we say x11() • dev.list() - list currently opened graphics devices • dev.cur() - list identifier for the current graphics device • dev.off() - close the current graphics window • A simple plotting example > x<-rnorm(100) > y<-rnorm(100) > plot(x,y) BINF634 - Perl and R

  12. High-level Graphics Functions • win.graph(), x11() • All Examples of Calls to Launch Graphics Window • A simple example • > x = rnorm(100) • > win.graph() • > hist(x) BINF634 - Perl and R

  13. Plotting Functions That Are Useful for One-dimensional Data • barplot- Creates a Bar Plot • boxplot- Creates Side-by-Side Boxplots • hist- Creates a Histogram • dotchart- Creates a Dot Chart • pie- Creates a Pie Chart • Note - These commands along with the commands on the next several slides are all high-level graphics calls. BINF634 - Perl and R

  14. A Simple Pie Chart > data = c(10,20,30) > labels = c("a", "b", "c") > pie(data,labels=labels) BINF634 - Perl and R

  15. Printing Graphics • File-Print Menu • Starting Printing Graphics Device • Postscript - Postscript • Pdf • Pictex - Latex • Windows - Metafile • png - PNG bitmap device • Jpeg - JPEG bitmap device • Bmp - BMP bitmap device • Xfig - Device for XFIGgraphics file format BINF634 - Perl and R

  16. Capturing Graphics to a jpeg File jpeg(file=“junk.jpg”) plot(x,y,pch=“*”) dev.off() BINF634 - Perl and R

  17. Alternative Screen Printing Approach #plot in an x11 or wingraph window and then write the output to a file > dev.print(bmp, file="myplot.bmp", width=1024, height=768) BINF634 - Perl and R

  18. Call R from Perl use Statistics::R; # Create a communication bridge with R and start R my $R = Statistics::R->new(); # Run simple R commands my $output_file = "file.ps"; $R->run(qq`postscript("$output_file" , horizontal=FALSE , width=500 , height=500 , pointsize=1)`); $R->run(q`plot(c(1, 5, 10), type = "l")`); $R->run(q`dev.off()`); BINF634 - Perl and R

  19. q and qq • q acts the same as single quotes so we do not have variable interpolation and it ignores single quotes • qq used to interpolate variables but to ignore double quotes BINF634 - Perl and R

  20. Communicating With R use Statistics::R; # Create a communication bridge with R and start R my $R = Statistics::R->new(); # Pass and retrieve data (scalars or arrays) my $input_value = 1; $R->set('x', $input_value); $R->run(q`y <- x^2`); my $output_value = $R->get('y'); print "y = $output_value\n"; $R->stop(); BINF634 - Perl and R

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