liebermeister
commented
6 years ago Dear Pierre,
thank you for your nice and encouraging words!
For details about the arrangement, it is probably best to contact Jörg Bernhardt, who developed the software. As far as I remember, the software initialises the placement of cells with one specific arrangement, one that we defined at some point as a "prototype". Since genes are linked (also between different species) via Kegg Orthology identifiers, the maps should, in theory, look similar for different organisms. However, this only holds for the large-scale structure (e.g. placement of large areas such as "metabolism"). The smaller structures (and individual polygons) can vary wildly, depending on what arrangement fits best the other constraints imposed by the algorithm (e.g., polygons should be preferably round, not elongated). For more details (e.g., whether or not the poylgons are "pulled" towards this prototype arrangement also during the optimisation run), Jörg is the right person to ask.
If I can be helpful in any other way, please write me again.
Best regards, Wolf
Good day Dr. Liebermeister,
I really appreciate your Proteomaps tools, and find myself using its online version quite often for visualizing my results. However, One question occured to me, for which i could not find an answer in your code (probably because I did not know where to look for it): How is the position of the polygons defined ? More specifically, for example, is my 'Translation' for E. coli always going to be top-right ? Is it organism dependent ? The question stems from the fact that ultimately I would like to compare proteomaps coming from different sources, and I would like to know if they will correlate visually.
Thank you for your help Best, Pierre