Difference between revisions of "Gnuplot/C2/Run-gnuplot-from-Perl-script/English"

Title Slide

Learning Objectives

• Statistical summary from gnuplot for datasets using Perl script
• Files containing only outliers for labeling box plot and
• A gnuplot graph, with multiple box plots with labeled outliers

System and Software Requirement

• gnuplot v 5.2.6
• Perl v 5.22 and
• Gedit v 3.18

Pre-requisites

[1]

• Learner must be familiar with the basics of gnuplot and Perl.
• For prerequisite gnuplot and Perl tutorials, please visit this site.

Code Files

Please download and extract the files.

Make a copy and use them while practising.

Download Link

[2]

Let’s open stat1.txt in any text editor. I will open in gedit.

First column is a row number.

The second column is y-data and third column is x-data.

Open a terminal.

Default extension of a Perl file is pl.

This opens the stats.pl file in gedit text editor.

You may use the text editor of your choice.

First line is the header and is essential for a Perl program.

It is called a shebang line.

use strict ; use warnings; and press Enter.

I will use the strict mode here.

Use warnings will generate warnings, if there are any errors in the program.

Note that the commands end with a semi colon.

my @filelist;

my $statfile;

my $label ;

my $upperlimit ;

my @dataarray ;

my @key ;

my @value ;

my @quarts ;

my $PROGRAM ;

my $GP ;

my $add;

my $linearray;

and press Enter.

The role of each variable will be explained as and when they appear.

The @ sign indicates that the variable is an array.

@filelist=('stat1.txt', 'stat2.txt', 'stat3.txt') ;

and press Enter.

foreach my $n (@filelist) { and press Enter.

press Enter.

This file will store the statistical data generated by gnuplot stats command.

open my $PROGRAM, '|-', 'gnuplot'

or die "Couldn't pipe to gnuplot: $!";

and press Enter.

If Perl is not able to access gnuplot, it will give the warning message as seen.

say {$PROGRAM} "set print '$statfile' "; and press Enter.

say {$PROGRAM} "stats '$n' using 2 "; close $PROGRAM; } press Enter.

The foreach loop runs the stats command for all input files in gnuplot.

Then, close the for loop.

Go to terminal.

Add in video type dir for windows users.

The newly created files have dot stat extension.

I will clear the screen for clarity.

Enter the command as seen here.

Lower and upper quartile values are displayed here.

Click on the X button to close the file.

let us close the text editor.

Go back to the script file in the text editor, to edit it.

foreach my $n (@filelist)

{

press Enter.

Use one more foreach loop to extract the quartiles and calculate the box range.

press Enter.

open (Statisticsfile , $statfile) ; press Enter.

while (my $limit = <Statisticsfile>) {

chomp $limit ; and press Enter.

let's delete the new line character at the end of the line with chomp command.

@dataarray = split(/\t/,$limit); } press Enter.

Store the split data in an array with the push command.

Close the while loop.

push(@key,$dataarray[0]);

push(@value,$dataarray[1]);

} press Enter.

$upperlimit = $value[21] + 1.5 * ($value[21]-$value[19]) ; press Enter.

We are using the values generated in the statistical summary file for this.

Hover mouse next to quartile range lines.

The Lower quartile value is seen in line 20 of the file.

User must find the relevant line numbers for the quartile range in your file.

Line Number in Statistical Summary File

The values are generated in line numbers 19 and 21.

and press Enter.

The push command stores the variables into an array.

We are interested in labeling values, which are above the box range.

highlight the lines.

$upperlimit = $value[21] + 1.5 * ($value[21]-$value[19]) ;

Hence I have used 19 and 21. instead of 20 and 22 to calculate upper box limit.

and press Enter.

and press Enter.

my @linearray = split (/\t/,$add); and press Enter.

I will also define an array for each line in the input file.

$label= $n.".label"; and press Enter.

open (OUT4,'>>', $label) ; and press Enter.

Make sure to open the file in append mode, to write all the outlier data points.

if ($linearray[1] > $upperlimit) { and press Enter.

print OUT4 "$linearray[0] \t $linearray[1] \t $linearray[2] \n " ; } and press Enter.

Close the if loop braces.

I will not print the outliers below the lower box limit here.

} } and press Enter.

@dataarray = (); @key = (); @value = (); and press Enter.

{ open(GP, "| gnuplot") or die "Error while piping to Gnuplot: $! \n"; print GP << "Gnuplot-end"; and press Enter.

set term svg set output 'boxplot-labeled.svg' and press Enter.

Specify a filename for the output file as seen.

set font "times,5" and press Enter.

set xtics ("stat1" 1, "stat2" 2, "stat3" 3) and press Enter.

set style data boxplot set xrange[0:4] and press Enter.

I will set x-axis range from 0 to 4.

plot 'stat1.txt' using (1):2 notitle, 'stat1.txt.label' using (1):2:3 with labels notitle offset 2,0, 'stat2.txt' using (2):2 notitle, "stat2.txt.label" using (2):2:3 with labels notitle offset 2,0, 'stat3.txt' using (3):2 notitle, 'stat3.txt.label' using (3):2:3 with labels notitle offset 3,0

and press Enter.

Add the labels using the newly generated files in the commands.

The three input files and the 3 outlier files are plotted here.

The offset gives a gap between the symbol and label.

Gnuplot-end close (GP) ; } and press Enter.

Go to the terminal.

Type, ./stats.pl and press Enter.

Type ls

Type the command as seen here to run the Perl script.

Type ls to list the commands files that are in the directory.

Since the path is Desktop, the output file is generated in the Desktop directory.

Other Programming Languages

• You may use C, Java, python or another language of your choice to program.
• If so, write the program accordingly.
• You may also use dataset of your choice.

Summary

In this tutorial, we generated,

• Statistical summary from gnuplot using Perl script
• Datafiles containing only outlier data points in box plot
• Plotted multiple box plots in a graphical window

Summary

• Specified the position of each box plot on x-axis
• Labeled the outliers in the box plot

Assignment

• Three files are provided in the Codes files link for assignment.
• Using the files generate box plot and label the outliers in the graph.

Modify the script to incorporate the correct file names.

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Acknowledgement