Once you have visualized your data on pathways
of interest, you can export the results to multiple graphical formats in
GenMAPP, such as .jpg, .bmp and html. This tutorial describes how to create
high-quality figures of the visualization for publications and presentations.
Optimizing color and display
The colors you have chosen for visualization of your data in GenMAPP may not
be optimized for display purposes. Certain color choices work better for printed
materials than others, so you may need to alter the
Color Sets for your data.
Below are a few rules of thumb for selecting optimal colors for display:
Avoid darker shades since they tend to cause bleeding and obscure gene
labels.
Avoid using shades of different colors that are too similar in terms of
color saturation, since they will be hard to distinguish if the figure is
printed or displayed in grayscale.
Avoid red and green since people with red-green color blindness will not
be able to distinguish the two.
Saving as PDF
Open the pathway of interest in GenMAPP.
Select the desired
Color Set Criteria
in the Color Set Criteria drop-down menu.
Customize the display of the Legend
under Tools>Options>Legend.
Check that the Legend does not overlap with any pathway objects.
Select whether or not to show the
MAPP Information Area,
under Tools>Options>Legend.
Check the layout of the pathway and make any final changes.
Under File>Print, select Adobe PDF in the printer drop-down
to export the pathway in Adobe PDF format.
Saving MAPP as PDF
Manipulating the figure in Illustrator
The PDF-formatted image may need some cleanup before it is ready, depending on
the final purpose of the figure. The cleanup is best done in Adobe Illustrator.
Open the PDF-formatted figure in Adobe Illustrator.
Review the figure to identify and fix any problems with the graphics or
layout of the figure. Common problems include:
- Brackets are not represented properly
- Gene boxes overlap the Gene Value displayed next to each gene box
- Arrow heads are not represented properly
Add any additional information you want to include in the figure, such
as figure legend or explanations.
Save the file as an Adobe Illustrator file for backup purposes.
To save the file for presentations/publications, save the file as a jpg
Do you have comments or questions about this tutorial? Contact
GenMAPP Support.