Cytoscape Layout Tools

this is satis cape 371 and I'm going to demonstrate layouts and the node layout tool I have already opened the yeast

perturbation sample network and switched the style to a consistent node fill just to make the nodes easier to see alright

the layout menu at the top will show you all the default layouts that are available inside escape in addition to layouts that come from apps that are

installed and a special case for the yfiles app which requires you to upon first installation agree to a license

and then you'll see the Y files layouts in addition just to demonstrate a few of these in this top section are the most

basic layouts circular layout as perhaps interesting it tries to find the most interconnected group and for it to form

the first ring and the circle layout and then there's a second layer of nodes connected to those at cetera as you zoom out

there's also under the layout menu a attribute circle layout and here for example you can choose any of the attributes you have loaded degree is a

common choice and it will lay out all of the connected nodes in a single a single circuit circular layout and in this case

they're ordered by degree starting in the six o'clock position and going clockwise from largest to smallest

degree again under the layout menu there is the perfuse force-directed layout

this is a common choice and it gives you the original layout provided with the

sample network for example and I'll show one of the Y files organic layouts that one's popular and it does a nice job of

force-directed layout with some additional spacing Q's added in and the final example of

layouts will be an edge weighted spring and bedded layout that will give you something like this so slight differences in those last debris that

are all spring based force-directed layouts that you can play with now the final thing I want to demonstrate is the

node layout tools so if we zoom in to a particular area you'll see that sometimes there's overlapping in the nodes and the node layout tool is a

handy way to fix that without having to manually move each node and fix it so again under layouts at the top node

layout tools that will open this extra panel here in the lower left and if I

have nothing selected I can use this

scaling feature to dramatically expand or condense the layout as is and then if

you zoom into an area maybe the layouts pretty good except for just in one area you can highlight a few notes and as long as selected only is checked you can

expand and condense just those nodes again without having to manually bias where things are laid out so it might space those out like that there's all

the align distribute and stack options that you'd expect to see whenever you have one or more node selected and then if i zoom out again another nice feature

is rotation this will let you rotate the entire layout but very importantly no matter how you rotate you'll notice the labels are staying horizontal to

maintain legibility so that's a nice way to fit and network into a portrait or layout format depending on what you're looking for