Improving layout is hidden

[vw253]

Everyone is having trouble finding this, and knowing what it means.

A prominent button "improve layout" would be really useful, as you need to do this to most networks initially to make it biologically "readable".

Even better if it happened automatically until the display was optimised. Or if that was not possible, could the optimisation run to completion when selected once. For instance to get the "regulation of cell cycle" to optimize fully, you need to select "force directed" over twenty times (we lost count)

[vw253]

and... This is really more about optimising the display than choosing the layout option. Maybe there should be a much more prominent button to “optimise display” at any time.

[Dan Bean]

I've tweaked the layout algorithm to get (I think) a much better layout in the first place, compare live vs dev e.g.:

• old: http://www.esyn.org/builder.php?type=Graph&term=GO:0051276&interactionType=physical&source=pombase&includeInteractors=false
• new: http://www.esyn.org/dev/builder.php?type=Graph&term=GO:0051276&interactionType=physical&source=pombase&includeInteractors=false

I also made a new option for the force directed layout - so now we have "improve the current layout" and "make a new layout from scratch" which are both under the layouts tab for now.

Unfortunately the way the algorithm works we can't determine how long it will run for, all we can do is set the maximum time it's allowed to run. I've increased that from 400ms to 10000ms when a new layout is generated.

[vw253]

I don't know what you did but it is orders of magnitude better. Much easier to read the biology. Cheers!

Val