In this lab, you will practice using Pedfiddler, a collection of programs that allows you to create a professional-looking pedigree document from a list file. You will begin by using Pedfiddler on a list file that has already been made, but your final work will be on a list file that you create yourself. If, in doing this lab, you have any questions or need any help, please feel free to email me at eathomp@u.washington.edu.
A. First check that you can access the Pedfiddler graphics.:
Pedfiddler is a graphics package. The pfiddler command in Pedfiddler should bring up an interactive graphics window.
1) First try
% which pfiddler
To check whether your path is correctly set -- it should be, from Lab 1.
If your computer cannot find pfiddler go back to the
Getting started information.
2) Next try
% pfiddler
This should bring up a window on your machine. It won't do anything else
yet: no problem.
Remember do NOT type the ``%'' -- this is just the prompt sign on your
computer -- nowadays it is likely a ``$'' sign instead.
If you are working off-site, or on a windows machine, you may have problems.
If you are using ssh on Unix/Linux
and it complains about ``MAGIC COOKIE'' try
ssh -X.
Otherwise, you may prefer to
download and install your own version of the
Pedfiddler package on your laptop or local machine.
This is not hard, and a zip file of Windows executables is available, -- see
the last link on the download table at the bottom of the
Pedfiddler page.
B. Practising Using
Pedfiddler:
1.
Copy the practice pedigree list file into your directory (or, of course to
your local machine, if you decided to have your own copy of the software).
A
practice pedigree list file can be found
here.
When you click on this link, you should see a page with a 15-member pedigree
in the, by now, familiar format, but without the extra MORGAN parameter
statements.
Each row on the page represents a different individual. The
first number in each row is that individual’s id number. The second and third
numbers are the id numbers of the individual’s parents. The number zero is
reserved for a parent that is not included in the pedigree.
The fourth number
tells the individual’s gender (1 = male, 2 = female).
The fifth column, disease
status, is not relevant for this week’s lab.
You
need to copy the practice file
into your b550 directory. I am going to call the
file jvped.dat, but you may choose your own name.
2. Import your file into Pedfiddler and into the pedc format (so we will be able to manipulate it using pfiddler).
Bring up pfiddler again:
% pfiddler &
There are some other options in the box -- I would keep them just as they
are!
Now, hopefully, your pfiddler window is showing a pedigree, but
it may look a bit of a mess. Never mind! Continue to step 3 below.
If you are having problems with your input files that
you cannot understand: click here for
possible reason and help.
Note that if you want to bring up pfiddler with an already created
pedc file, it is easiest to just say:
% pfiddler filename &
% pfiddler jvped.pedc &
Again the & is to run the file in background: that is, you can still do things
in your regular command window, while the pfiddler
graphics window is up.
This is not essential, but useful.
3. Use pfiddler
to make your pedigree pretty.
Remember you do not type the ``%'' -- this is just the computer's prompt.
However you do type the ``&'': this tells the computer to run the
pfiddler window in background, so you can continue to use your regular
command window.
Now in the pfiddler window,
under the File menu, click on the Import option, and under that
Text. This should
bring up a small window. Enter the name of your text file in the
box -- replace the default ``input.txt'' with the name of
your input pedigree listing
jvped.dat. (Your file can be called whatever
you like.) Enter something such as jvped.pedc in the output file box:
it does not have to end
.pedc, but it may be helpful to keep this convention, so you
remember it is a Pedfiddler format file.
Or, in our case:
Once
in pfiddler, you have a lot of options. You can move your individuals
(or marriage nodes) by dragging them with the left-most button on your mouse
(the default is horizontal motion, but you can chose other options under the
“Motion” menu). You will definitely want to move your individuals
because pfiddler
often puts individuals on top of each other. Also the current version has lines crossing. By moving them around, you can make it look nice and tidy,
like the copies of this same pedigree in the audio lectures.
To change the color of an
individual, try clicking on that individual with the right-most button on your
mouse. Once you have chosen the color for an individual, you can make all the
descendents of that individual the same color by going to the edit menu to
“colors” and choosing “drop downwards”, then left-click on the individual.
“Drop Upwards” works similarly. If the computer network is slow,
it make take a second or two for the colors to change: do not panic and start
clicking wildly. Experiment for a while until you feel
comfortable using the program and like the look of the pedigree.
(Note you may get various warning messages in your regular terminal window
as you move things in the pfiddler window: just ignore these.
Note also that not all mice on all
computers work the same: I have edited the left/right
in the above parag., to work for the current pfiddler with my current
desktop. If left does not work, try right -- and vice versa.)
Identifying individuals:
Your plot (see below) will show the ID numbers of individuals, but the
pfiddler window does not.
If you want to see which individual is which in the pfiddler window,
move your mouse over the individual (click left, if necessary),
and the ID and other info
(in any) shows in the boxes at the top right of the window. Neat!
Save your file when you are
finished: use the File menu in the upper left corner of your
pfiddler window. You can save under the same name using Save,
or under a different one such as jvped2.pedc using the
Save as option.
Quit from pfiddler by using the Quit under the File
menu in your pfiddler window. (This is the simplest way:
there are others.) WAIT: Don't quit yet.
4.
Make a PostScript or EPS file from your pedigree.
Use the Make Eps option under
the File menu in the pfiddler window. If you did
quit out of the
pfiddler, simply restart pfiddler --
remember to this time use the
new version of your pedigree (for example jvped_new.pedc),
which hopefully you did save:
% pfiddler jvped_new.pedc &
When you
click on Make Eps an additional small window will open
showing you several options for sizes of your plots and icons, line
thickness, and space to add a title for your plot.
The plot does include the ID numbers on it (by default). The switch to
toggle this on/off in the MakeEPS window is the "identify" one.
You can (maybe)
use ghostview to look at
your finished pedigree by typing:
% ggv jvped.eps
assuming, of course, that you have output the file under the
name jvped.eps. (Remember the unix ls command, to list the
files in your directory.)
In fact, once you have the
jvped.eps file, it is probably easiest to download it to
your own desktop/laptop (using sftp) in order to
view it. If you do not have ghostview locally, you can first use
the Unix utility ps2pdf
to turn your file into a PDF file:
% ps2pdf jvped.eps
C. Your Assignment.
1. Take the pedigree file (without errors!) that you set up in lab 1. Make a copy without the MORGAN headings, so it is a straight text file of 4 (probably) columns -- looking like the jvped.dat file (except without the fifth column).
Reminder from Lab 1: The pedigree file should be about 20 individuals, including at least one pair of bilateral relatives other than siblings (e.g. double first cousins) and at least one inbred individual. If you do not have one from Lab-1, make it now!
Note: It may be Pedfiddler will only accept numerical ID's. (That used to be true, and I have not had time to check.) If so, then those who had neat pedigrees with non-numerical ID's will have to rename people -- sorry!
2. Import your text pedigree file into
pfiddler, as above,
and move individuals, and use colors, to make it look good.
3. Create an EPS version of your pedigree using the
pfiddler Make Eps option. You may turn in either an EPS
or PDF file. The
version you turn in should have a title, suitable line thickness, and icons
larger than 9 pt. It should be in color.