genetic mapcreator

Use

Input Data Format

The input data format for Genetic MapCreator is a plain text file consisting of lines of marker or feature information. Each line of the input data file should contain a marker name, a coordinate, and an optional rendering hint. Each of these three items should be separated by either a space or a tab character. A blank line is used to separate multiple linkage groups.

Absolute Coordinates

Sample Absolute Coordinates
marker1100000
marker2200000
marker3250000
If absolute coordinates are used, they must appear in order starting from the smallest coordinate and ending with the largest coordinate.

Relative Distances

Sample Relative Distances
marker10.34
marker20.1
marker3
If relative distances are used, the value on each line represents the distance between this marker and the one on the next line. The last line should not contain a distance (because there will not be markers following it.

For radiation hybrid data, the distance between markers is often in units of Ray (R). For genetic maps this data is often in Morgans (M). If there is more than one linkage group per chromosome an empty line should be left between the data sets.

Rendering Hints

An optional third or final column may be added to provide a rendering hint for that marker. A rendering hint is a string of one or more characters representing either a color (a lower case letter) and/or a font modification (an upper case letter).

Color Rendering HintsFont Rendering Hints
w (white)
r (red)
o (orange)
y (yellow)
g (green)
c (cyan)
b (blue)
i (indigo)
v (violet)
m (magenta)
B (bold)
I (italics)
U (underline)
R (reverse render)

Sample Input

The following table shows example input data on the left and the sample output image on the right. This data set contains 3 linkage groups using multiple marker names and many rendering hints.

SW34 NW64		.34	U
SW45			.1
SW7654 SD45 GP-9	.54	r
SW6784				yB

SW893			.43 	Uv
ING_A			.654	gB
S0345			.987	bIR
S0879

SWR5784			.345 	B
S0345			.45	iBI
SW9087			.32
SW1 SW2 SW3 SW4			U
Sample Gene Map File

In the above example, notice the following:

The above sample data may be downloaded here.

Output Preferences for Genetic MapCreator

Scale

There are two things that can potentially affect the height of an image generated by Genetic MapCreator:
  1. The number of marker names and the size of the font.
  2. The vertical scale of the graph.
The value used for scale will affect the vertical scale of the graph.

Pointsize

The pointsize will affect the image height of the map. If there are many markers in close proximity, the map will be longer as the marker names are listed so that there is no overlap.

Default text color

This color will be used to draw all marker names unless overridden with a rendering hint.

Transparent background

This might be good to use if you are putting the generated image into a web page. NOTE: Internet Explorer does not fully support tranaparent PNG images.

A tic mark every ___ units

This is the spacing between minor tic marks.

A label every ___ tic marks

This defines the frequence of the tic mark labels. It is often desireable to make the labels appear in "even" units. Therefore, if the tic unit is something like 0.2 or 200, it would make sense to display a label every 5 tic marks. Likewise, if the tic unit was something like 0.5 or 50, it would make sense to display a label every 2 or 4 tic marks.

Generate a client-side image map data

If set to 'yes', the HTML code will be generated for a client-side image map. This will allow you to place your map into a web page such that users can click on the marker names and be presented with further information of your choice. The HTML file name will be based on the name of the image file. For example, if you save your image file as "sample.png", and HTML file named "sample.html" would also be generated.

Image map URL

If the previous option is ticked, this path will be used in the generation of the client-side image map. In general, it is easiest to handle the results of a client-side image map by using a dynamically created page such as an ASP or CGI program.

The example to the right is a "clickable" map. As you mouse over the marker names, notice the URL in your status bar. If you "click" on a marker name, a sample CGI program will tell you what marker you selected.