Example 6 - Map with glyphs



Glyphs allows to color species, compartments or pathways with user’s provided images. The extension of the images have to be PNG and the files have to be inside directory named glyphs. The images are assigned to the elements by term:
Glyph: glyphs/image-name.png

Download the example of the map colored with glyphs and upload it to MINERVA. That file is an archive, which contains two images in the glyphs directory and the CellDesigner map. Glyphs can be used both to color submap and main map (if a project is advanced).
Below image presents the view of map.

Note: By default MINERVA draws reactions lines in the back of the compartment (so glyph covers it). To see reactions on the glyph, you need to set up the transparency of the compartment and Z-Index correctly.

See below the properties of the glyphs map:

  • Compartment cell is colored by glyph g1.

  • Compartment cell has SemanticZoomLevelTransparency: 0.

  • Compartment cell has Z-Index: -2, here it is at the bottom of the map. (For elements and reactions which are not assigned with Z-Index, MINERVA by default give them positive values so they have to be at the front of the compartment.)

  • Pathway SNCA translation and protein PRKN are colored by glyph g2.

  • Pathway SNCA translation has SemanticZoomLevelTransparency: 1.

  • Pathway SNCA translation has Z-Index: -1. It is at front of the compartment cell, but still Z-Index is negative value, what makes the elements and reactions displayed at the front of it.


CellDesigner layers visible/invisible