Getting started with PED
Input and Edit window revisited
By now you should have an idea how the two windows work
- When you launch PED, you are in Input mode
You select a (human) symbol (you cannot select a line), then an action (press a button) - In Edit mode, you first select a symbol from the symbol bar,
then click at the cell in the window, where the symbol is to be drawn - You paste the pedigree from the input window to the edit window by
- You cannot re-import a pedigree from the edit window in the input window
- You can edit a symbol, the surrounding text, arrows, deceased marker ... in both modes by right click on the symbol
- You can switch between both windows by [Ctrl]+Q and [Ctrl]+W, or
- Export / Import the family as / from a CSV, PIP, or LINKAGE file in input mode
(press the Import or Export button, respectively - Save / open the layout in the edit window as a PED file.
(Menu File-- Open or Save as ...)
- Export the layout from the edit windowas a WMF file
that any office program can import
(Menu File -- Save as ...; now enter SomeName.WMF)
Edit annotations
We switch to Input mode ([Ctrl]+Q), and import the pedigree (press the Import button) we saved on page 3. Now paste the pedigree to the Edit window:
In Edit window, press [Ctrl]+N, or select the appropriate menu item
The annotation window opens. Enter some text. Select a relative font size, and an alignment relative to a cell:
Press OK. Nothing happens ... Now click on the T button in the symbol bar:
The text you entered is treated as any other (human or line) symbol. You choose the T button to select a text just entered in the annotation window, and you click on a cell that will be the "container" for the text:
Delete an annotation in the drawing
Click on the empty symbol button (first column / second row) in the symbol bar. Click on the cell in the drawing where the "container" of the text is located. If you are unsure where this is, show all text containers (reverse these cells):
The cell containing the text is reversed:
Now with the "empty" cell in the symbol bar selected, click on the reversed cell in the window:
Press [Ctrl]+R to redraw, thus removing the remnants of the previously deleted text.
Options in Edit and Input mode
If you choose (in Input mode) Input window - Options - More ... or (in Edit mode) Screen - View, you get the following dialog:
These options should be rather self explaining. If in doubt, please press the Help button.
Adding a legend
You can add a legend manually: Click at the appropriate symbol in the symbol bar, click on the edit window to draw the symbol, right click on the symbol, and enter the appropriate legend. As an alternative, you can do it automatically:
Now you get a , well, simple legend for a simple pedigree:
PED scans all symbols in the pedigree, and shows each symbol that is not white / empty. The legend text is taken from the phenotype menu. Since we previously chose "left filled" from the phenotype menu, this is what the legend will say:
now you can right click on this symbol to edit the legend text:
This is the legend:
Consider editing input text labels and phenotype menu items
... when data from pedigrees entered by different persons should be collected in a single database.
This does not look like a big deal with this simple pedigree from above. But consider counceling cancer families. You can edit the phenotypes menu items as well as all corresponding symbols just as you like (for details take a look at the how-to resources). Then phenotype #4 is no longer "left filled" but, say, "HNPCC". And phenotype #26 may be not just "bottom left white", but a red symbol labelled "breast cancer", and so on. Even easier to change are the labels of the "Text and haplotypes" dialog:
Then in the dialog no longer "Text 1" but a more meaningful "First name" or "day of birth" will be displayed, and instead of "M1", e.g, the name of the marker you used:
Now, when you right click on a symbol in the input or in the edit window, more meaningful labels for the input fields will be dsplayed:
When these edited labels and phenotype menu items are made available to all PED useres involved in the same investigation (even at different locations), they all can export their pedigrees, e.g. as a CSV file, where each family member has an unique ID (preserved even after multiple im-/exports), and all exported files carry the same kind of information in their respective columns.
The file menu: Save the pedigree as an editable layout (PED) file or as Windows metafile (WMF) for import into a presentation or text program
From the file menu select Save as... and enter the name of the pedigree. A file suffix of "PED" will it make editable in the edit window in PED. A file suffix "WMF" will create a Windows Metafile:
Enter the name of the pedigree. Please do not miss to enter the suffix (ped or wmf) as well:
If you save as a Metafile, you may want to have a colored background:
Press OK. Now create a new text document (This is an example with OpenOffice.org), and insert a picture from file:
Finally, here is the metafile (it will work in MS Word, or in presentation programs like MS Powerpoint as well...), ready to be resized, from stamp to poster size.
No need to mention ...
... PED can print pedigrees at any size on each paper size. It is nice to print a large pedigree in poster size - but most of the time you probably print a pedigree on your own office printer. PED uses always one sheet of paper, no matter what the paper size is.
Thank you for reading Getting started !
Now you should know enough about PED to start drawing. Later on, you may want to take a look at the Import / Export part, the How-To resources, and the FAQs.