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Starting from the example given in the documentation that you could have bothered to read by typing desolve_system_rk4? :

sage: from sage.calculus.desolvers import desolve_system_rk4
sage: x,y,t=var('x y t')
sage: P=desolve_system_rk4([x*(1-y),-y*(1-x)],[x,y],ics=[0,0.5,2],ivar=t,end_points=20)

you can see that the solution P is a list of [t, x, y] triplets. You can display the x and y functions by :

sage: line2d([[i, j] for i, j, k in P])
sage: line2d([[i, k] for i, j, k in P])

(line2d interpolates between the points that list_plot displays, which is aesthetically more pleasing).Your phase trajectory can therefore be displayed by :

sage: line2d([[j,k] for i, j, k in P])