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.
|Sample Absolute Coordinates|
If absolute coordinates are used, they must appear in order starting from
the smallest coordinate and ending with the largest coordinate.
|Sample Relative Distances|
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.
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 Hints||Font Rendering Hints|
R (reverse render)
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
SW7654 SD45 GP-9 .54 r
SW893 .43 Uv
ING_A .654 gB
S0345 .987 bIR
SWR5784 .345 B
S0345 .45 iBI
SW1 SW2 SW3 SW4 U
In the above example, notice the following:
- There are three linkage groups each separated by a blank line.
- More than one marker name can be placed on each line.
- Since relative distances are provided, the last line of each linkage group does not require a distance.
- When no rendering hint is provided, the marker is drawn in black using a "normal" font.
The above sample data may be downloaded here
Output Preferences for Genetic MapCreator
There are two things that can potentially affect the height of an image
generated by Genetic MapCreator:
- The number of marker names and the size of the font.
- The vertical scale of the graph.
The value used for scale will affect the vertical scale of the graph.
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.
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.