Positive current and negative current is relative.
Example: current in a resistor =+, cut the resistor out and flip it 180 and put it back, =-.
Also: If the transistor's collector current is (+) then the emitter current is (-). flow into/out of
If you don't like the way the wave for looks right click on the name of the trace. change the name from I(l2) to -I(l2) this will invert the trace. (math, negative current in l2) This does not really change anything but it helps your head.
Another idea. Say you are looking at base current and collector current of a transistor. The collector current is 100x that of the base so you can hardly see the small base current. Rename the base current by adding 100*ahead of the name or *100 after the name. Now the graph will display 100x the base current and the collector current.
There are many math options.