The University of Arizona
FPC Contig Display demo  
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Written by Fred Engler


Coloring entities
Creating a new track
Resizing a track
Moving a track
Hiding entities
Filtering by remark
Removing a track
Row policies
Saving the contig layout
Viewing help

Introduction Back to top

Please download the fpc file used in this demo by clicking here.
Untar the file in the desired directory with:
   tar zxvf ctgdemo.tar.gz
Start FPC with the demo file by typing
   fpc ctgdemo
on the command line. Follow the normal steps to open contig 1 (the only contig in the project). You are presented with the new contig display:

The main part of the window is broken into four sections. Each of these sections is called a track, and you determine exactly how many tracks are shown, and what is shown in each track. A track can contain either 1) markers, 2) clones, 3) remarks, 4) anchors or 5) sequence which has been aligned to the FPC map using the Draft Sequence Integration module. Use the horizontal scrollbar at the botton to scroll through the contig. You will notice that the bottom (anchor) track does not scroll; instead, a viewer (white area) moves over it, indicating which portion of the contig is currently shown. The ruler immediately above the scrollbar indicates the scale of the contig in CB (consensus band) units. Change the zoom in the top left, either by ckicking on the bar and moving it, or clicking in the space beside the bar. Click 'Whole' to see all clones made to fit in the currently viewable area. It will be quite dense! Zoom out to a more reasonable scale.

Coloring entities Back to top

Right-click on the first (marker) track. A menu will appear, giving you three options: 'Edit track properties', 'Remove track', and 'Close contig'. Select 'Edit track properties'. A window opens, showing you, among other things, which filters are currently applied to the track:

In the 'Selected Filter Edit' box, click on the first option menu (under the 'Type' column). A list of marker types is shown. Select 'eMrk' from the list. A new filter is created, as shown by the new row in the filters list. Next, select 'blue' from the 'Color' option menu. When you are done, click on the 'Apply & Close' button. All markers of type eMrk are now colored blue!

Creating a new track Back to top

From the 'Add track' menu at the top, select 'New clone track'. A new track containing clones is created and appended to the bottom of the track window. Use the vertical scrollbar appearing on the right to move to it. Right-click on an empty part of the track (not on or close to a clone), and select 'Edit track properties' from the menu. If this is not an option, move the mouse a little, as you probably clicked too close to a clone. Click on the first row in the list, and select 'Finished' from the 'Status' option menu. Click 'Apply & Close'. The track now shows only clones that have a 'Finished' status!

Resizing a track Back to top

Move the mouse towards the bottom of the newly created track to where the cursor changes. Click and drag upwards with the mouse until the track is about one inch tall. Release the mouse button, and the track is resized to the new height.

Moving a track Back to top

Once again, open the Edit Track Properties window on the newly created track. We want to place this track immediately above the current clone track. Select '2' from the 'Track position' spin button at the top right. Click 'Apply & Close'. The track is now moved to the second position in the window.

Hiding entities Back to top

Open the Edit Track Properties window for the original clone track. Since the finished clones now have their own track, they no longer need to be shown in this track. Click on the second row in the list, and set the 'Color' option menu to 'Invisible'. Click 'Apply & Close'. The finished clones are no longer shown!

Filtering by remark Back to top

Open the Edit track Properties window for the finished clone track. In the 'Remark Substring' text box, type "Sasaki" and select 'Green' as the color. Click 'Apply & Close'. All clones containing 'Sasaki' in their remarks are colored green. This makes it easy to see which lab sequenced the clone.

Removing a track Back to top

Right-click on the remark track (2nd track from the bottom; should now be 4th from the top) and select 'Remove track'. You will be prompted whether you really want to remove the track. Click 'Yes'. The track is removed from the display. It can be recreated at any time via the 'Add track' menu.

Row policies Back to top

Notice that some clones are written on top of each other in the original clone track. This is because there are not enough rows to correctly display the clones with the current track height. One solution is to resize the track. Another is to allow a "per track" scrollbar (the one on the left). Open the Edit Track Properties window for the original clone track. From the 'Row Policy' box, select 'Automatic'. Click 'Apply & Close'. The clones will be reorganized so that none are written on top of each other. Use the vertical scrollbar on the left-hand side of the track to scroll through the clones. You may also try resizing the track. Experiment!

Searching Back to top

You can search for a substring of any entity in any of the current tracks, and all matches will be highlighted in orange (except for anchor tracks). Type "SOG" in the 'Search' text entry at the top of the window. You will see all markers with this string in their name highlighted. Experiment with other strings. To clear all highlights, select 'Clear all' from the 'Highlight' menu.

Saving the contig layout Back to top

You can store the way you have arranged the current contig. There are three ways to save layouts: 1) For this contig only, 2) For all contigs, and 3) For all contigs without a previously saved layout (Make this one the default layout). Either of the three works in our case. Select one option from the 'Layout' menu. The layout information is stored for the current session. If you want this layout when you reopen FPC, click on the 'Save .fpc' button on the Main Menu window. Otherwise, the previously saved (or default) layout will be used when the project is reopened.
Here is what the display should look like when you're done:

Viewing help Back to top

There are several help pages in FPC to guide you along. You can get to these by clicking on the 'Help' buttons (or 'Show help' from the 'Help' menu for the contig display). However, this requires that the FPCHELP environment variable be set to the location of the help file. For example, at AGCoL the help file is located in /home/agcol/fpc/, so we set the environment variable as follows:
setenv FPCHELP /home/agcol/fpc/
Set your FPCHELP to where it is located on your system. You may want to consider adding this line to your .cshrc file. If FPCHELP is not set, you will be prompted for the file location when you click on a help button.


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Last Modified Wednesday October 29, 2008 13:44 PM and 02 seconds