How to use TkMap


TkMap is a bioTk script for drawing and printing high quality output of genetic maps. TkMap reads in a framework map file and a confidence interval file in a simple text format and draws the implied map on a Tk canvas. This canvas may be resized, and the font used for drawing the marker labels changed. You can also generate encapsulated postscript from the map, either for printing or importing into a word processing package.

Making a linear map

Create a linear map file that lists the linear map markers one per line, in the correct map order. After each marker (except the last) list the distance from the marker to the next. Comment lines beginning with a ``#'' character and blank lines are ignored. Marker names ending with the ``*'' character are considered to be framework markers and are printed in boldface.

Here's a sample linear map:

EG0001    0.076
EG0002    0.048
EG0003    0.073
EG0004    0.024
EG0005    0.117
EG0006    0.058

EG0007    0.35
EG0008    0.091
EG0009    0.150
EG0010    0.199
EG0011    0.026
EG0012    0.183

This file can be loaded into TkMap via the File menu, clicking on File, then Load, then "Linear Map" brings up a dialog box which can be used to load the linear map file.

Here's a screen shot of the File Load menu. The file load dialog box is shown here.

Making a confidence interval map

The confidence interval map file also has a list of markers, but instead of each marker being associated with a distance, it is instead associated with an interval between two markers on the framework map. List the two framework map markers at the extremes of the interval to which the new marker is associated.

If several markers are associated to the same interval, you can specify all their names between quotes as the first item in a line.

Here is a sample confidence interval file:

EG0014	EG0001 EG0008
EG0015	EG0001 EG0003
EG0016	EG0003 EG0010
EG0017	EG0009 EG0013
EG0018	EG0005 EG0007
EG0019	EG0008 EG0012
EG0020	EG0004 EG0008
EG0021	EG0001 EG0007
EG0022	EG0008 EG0011

"EG0023, EG0024"	EG0001 EG0006

"EG0025, EG0026, EG0027, EG0028, EG0029"	EG0010 EG0013

Confidence interval files can be loaded into TkMap only after the linear map has been loaded. Select File, then Load, then "Confidence intervals" to load the file.

Here's the screen shot of TkMap after the above two files are loaded.

Changing the on screen appearance of a map

TkMap has several options that can be set by the user to change the appearance of the map. Clicking on the "Preferences" menu option, brings up a dialog box where the parameters can be edited.

Sets the width in pixels of the on screen map.
Sets the height in pixels of the on screen map.
Sets the width in pixels of the gap between the linear map and the confidence interval map.
Font size
Changes the point size of the font used for the marker labels.

After making any changes to the parameters, click the Apply button to see the effect.

Here's a small shot file of the preferences dialog.

Printing the map

After the map is prepared and the parameters are set, you can print the map with the File, Print menu option. This brings up another dialog box where the print options can be set. TkMap prints by generating an Encapsulated Postscript file that approximately matches the on screen map. The postscript file can be sent directly to the Unix print spooler (using lpr) or saved to a file for later printing or importing into another program.

Here's the screen shot of the Print dialog box.

Troglodita approved!

Humberto Ortiz Zuazaga

Most recent change: 2005/1/4 at 22:03
Generated with GTML