binf 634 fall 2013 - lec 11 visualization1 plan for tonight a synopsis of our progress through the...

BINF 634 Fall 2013 - Lec 11 Visualization 1

Plan for Tonight

A synopsis of our progress through the course

Lecture 11 Visualization in PERL

Lab 2

Based in Part on Previous Lecture of J. Grefenstette

Outline


Where We are and Where We are Going

Program 1, Program 2, turned in and graded Midterm turned in and graded Program 3 turned in, Program 4 assigned tonight

Program 4 due in two week (11/25/13) Quiz 1, Quiz 2, Quiz 3, Quiz 4, lab1 turned in and

graded Lab 2 assigned tonight (11/11/13)

Lab 2 Due next week 11/18/13 Take home final provided 11/25/13

Take home final due to me 12/16/13

Miles to go …


Data Visualization Numbers are well and good, but often we get more insight by

visualizing data

As always, it's a good idea to break the process down into individual steps:data analysis script => output file => plotting script

=> chart file

This can all be wrapped for Web access:CGI script to get user input =>data analysis script => output file => plotting script

=> chart file=> CGI script displays chart on web page

Viz strategyBased in Part on Previous Lecture of J. Grefenstette


GD::Graph

Created by Martien Verbruggen

GD::Graph is a Perl module to create charts using the GD module. The following classes for graphs with axes are defined:

GD::Graph::lines -- Create a line chart

GD::Graph::bars and GD::Graph::hbars-- Create a bar chart with vertical or horizontal bars.

GD::Graph::points-- Create an chart, displaying the data as points.

GD::Graph::linespoints-- Combination of lines and points.

GD::Graph::area-- Create a graph, representing the data as areas under a line.

GD::Graph::pie-- Create a pie chart.

GDBased in Part on Previous Lecture of J. Grefenstette

#!/usr/bin/perluse strict;use GD::Graph::bars;# File: bargraph.pl (based on http://linuxgazette.net/issue83/padala.html)

# All data arrays should have the same number of entriesmy @x = ("Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug",

"Sep", "Oct", "Nov", "Dec");my @y = (23, 5, 2, 20, 11, 33, 7, 31, 77, 18, 65, 52);

# create a 2-dimensional array, where row 1 is x and row 2 is ymy @data = (\@x, \@y);

#create a new bar graph object and give it size (in pixels)my $graph = GD::Graph::bars->new(500, 300);

# set graph features such as labels on the axes, title$graph->set( x_label=>'Month', y_label=>'Number of Hits',

title=>'Number of Hits in Each Month in 2002')or warn $graph->error;

# plot the data to create an image objectmy $image = $graph->plot(\@data) or die $graph->error;

# print the image as a PNG file formatopen IMG, ">hist.png" or die "Can't open hist.png\n";print IMG $image->png;exit; 5BINF 634 Fall 2013 - Lec 11 Visualization



Output

% open hist.png


#!/usr/bin/perluse strict;use CGI qw(:standard);use GD::Graph::bars;# File: bargraph.cgi

# All data arrays should have the same number of entriesmy @x = ("Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug",

"Sep", "Oct", "Nov", "Dec");my @y = (23, 5, 2, 20, 11, 33, 7, 31, 77, 18, 65, 52);






# print the image as a PNG file formatprint "Content-type: image/png\n\n";print $image->png;

7BINF 634 Fall 2013 - Lec 11 Visualization

Let’s create a web version !

GD


#!/usr/bin/perluse strict;use GD::Graph::bars;# File: bargraph2.pl

# read a file to get the data:my @x = (); my @y = (); open FH, "hist.dat" or die;while (<FH>) { my ($xval, $yval) = split; push @x, $xval; push @y, $yval }close FH;






# print the image as a PNG file formatopen IMG, ">hist.png" or die "Can't open hist.png\n";print IMG $image->png; 9

BINF 634 Fall 2013 - Lec 11 Visualization

Plotting points from a file.

GD



% cat hist.dat

Jan 23

Feb 5

Mar 2

Apr 20

May 11

Jun 33

Jul 7

Aug 31

Sep 77

Oct 18

Nov 65

Dec 52


#!/usr/bin/perluse strict;use GD::Graph::linespoints;# File: plot.plmy @x = (); my @y = ();

# read a file to get the data:open FH, "hist.dat" or die;while (<FH>) { my ($xval, $yval) = split; push @x, $xval; push @y, $yval }close FH;


#create a new bar graph object and give it size (in pixels)my $graph = GD::Graph::linespoints->new(500, 300);




# print the image as a PNG file formatopen IMG, ">out.png" or die "Can't open out.png\n";print IMG $image->png; 11BINF 634 Fall 2013 - Lec 11 Visualization

Creating a plot with lines and points.

GD


Getting the Chart on the Web This can all be wrapped for Web access:

CGI script to get user input (e.g., wrapper) =>data analysis script => output file => plotting script (e.g., plot.pl) => chart file (e.g.,

out.png) CGI script (wrapper) displays chart on web page

To display a file on the web, it has to be in a readable directory in the ~/public_html directory tree

1. Create a directory that can be written to by the web server process:

% mkdir ~/public_html/cgi-images% chmod 777 ~/public_html/cgi-images


GD


Getting the Chart on the Web2. In the wrapper, create the graphics file in the working directory3. Copy it to the images directory4. Display it using print img{src=>...}

use CGI qw(:standard); ...

# change to working directorymkdir $dir or die "Can't create directory $dir\n";chdir $dir or die "Can't change to directory $dir\n";

# create the data file for plottingsystem "cp /userhomes/faculty/jsolka/binf634/visualization/hist.dat $dir";

# run the plotting programsystem "/userhomes/faculty/jsolka/binf634/visualization/linegraph.pl";

# copy the output image to the web images directorysystem "cp out.png

/userhomes/faculty/jsolka/public_html/cgi-images/out.png";

# display image file on the web pageprint img {src=>"/jsolka/cgi-images/out.png"};


GD



Limitations to GD::Graph

GD::Graph is good for simple graphs but has some severe limits for scientific plotting

X-axis data assumed evenly spaced 2-dimensional Limited control over labels, arrows, etc.



gnuplot

gnuplot is an open source Unix application for creating high quality plots from data

http://www.gnuplot.info/ Runs interactively and in batch mode Interactive mode:

% gnuplot> plot sin(x)

gnuplotBased in Part on Previous Lecture of J. Grefenstette

gnuplot Batch mode

put commands into a file, for example, histogram.plt run gnuplot with the command file as argument

% gnuplot histogram.plt

% cat histogram.plt# file histogram.pltset xlabel "Length"set ylabel "Sequences"set title "Sequence Length Distribution"plot "plot.dat" with boxesexit


gnuplot



gnuplot accepts input files with an x,y pair on each line:

% cat plot.dat500 22550 14600 12650 13700 3750 7800 0850 7900 6950 31000 2


gnuplot gnuplot can create PNG format files, which work in all

common browsers

# file hist.plt# usage: gnuplot hist.plt

set output "hist.png" # name of output file

set terminal png medium mono # type of output file = PNG

set size 0.8, 0.8 # adjusts size of text

unset key # do not display key

set xlabel "Length" # x-axis label

set ylabel "Sequences" # y-axis label

set title "Sequence Length Distribution"

set style fill solid 1.0 # make boxes black

set boxwidth 0.9 relative # leave small space between boxes

plot "plot.dat" with boxes # plot the data file

exit


gnuplot


BINF 634 Fall 2013 - Lec 11 Visualization

20

Output


## File: hist3.plt# usage: gnuplot hist3.plt## assumes data is stored in “myplot.dat"#set terminal png # type of output file = PNGset output "hist3date.png" # name of output fileset title "Hits Per Month" # title of graphset xlabel "Months" 0,-1 # x-axis label (down 1 character)set ylabel "Hits" # y-axis labelset size 0.75,0.75 # reduce graph sizeunset key # do not display keyset boxwidth 0.9 relative # leave small space between boxesset style fill solid 1.0 # make boxes solidset xrange [0:13] # control size of x-axis

# fine tune labels on x axisset xtics rotate ("Jan" 1, "Feb" 2, "Mar" 3, "Apr" 4, "May" 5,

"Jun" 6, "Jul" 7, "Aug" 8, "Sep" 9, "Oct" 10, "Nov" 11, "Dec" 12)

# plot the data file, creating "hist.png"plot “myplot.dat" with boxes




gnuplot data file

% cat myplot.dat1 232 53 24 205 116 337 78 319 7710 1811 6512 52



hist.png


Getting the Chart on the Web2. In the wrapper, create the graphics file in the working directory3. Copy it to the images directory4. Display it using print img{src=>...}

use CGI qw(:standard);$ENV{PATH} = "/bin:/usr/bin:/usr/local/bin"; # for gnuplot ...

# change to working directorymkdir $dir or die "Can't create directory $dir\n";chdir $dir or die "Can't change to directory $dir\n";

# create the data file for plottingsystem "cp /userhomes/faculty/jsolka/binf634/visualization/plot.dat $dir";

# run the plotting programsystem "gnuplot /userhomes/faculty/jsolka/binf634/visualization/hist.plt";

# copy the output image to the web images directorysystem "cp hist.png /userhomes/faculty/jsolka/public_html/cgi-images/hist.png";

# display image file on the web pageprint img {src=>"/jsolka/cgi-images/hist.png"};


gnuplot


Perl Data Language (PDL)


http://pdl.perl.org/

PDL


A Few Discussions on PDL

The next several slides were adapted from the PDL tutorial by David Mertens at this URL

http://www.slideshare.net/dcmertens/p-lplot-talk


PDL



Adapted from David Mertens at this URLhttp://www.slideshare.net/dcmertens/p-lplot-talk

PDL




PDL


More information Online documentation for GD::Graph

% perldoc GD::Graph

Online doc for gnuplot% gnuplot> help

Also see: http://www.gnuplot.info PLplot

http://plplot.sourceforge.net/examples.php PDL



Summary


Homework and Reminders

Program 4 due next week 11/26/12 Lab 2 due by next week No more quizzes No more programming assignments Only the final

Read Chapter 11 Exercise 11.1 and 11.2

Reminders

binf 634 fall 2013 - lec 11 visualization1 plan for tonight a synopsis of our progress through the...

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