Difficult question, but a very worthwhile thing to try to "visualize." I agree with @commonhare 's comments on your question: trial and error using a spectral analyzer would be an effective way to increase your understanding as well as your aural intuition. A similar procedure with your guitar and amp could also be helpful:
Try setting all of your tone knobs to a neutral position, and, for now, use all of your pickups, or at least both the bridge and neck pickups. Strum a few chords, play a few melodic lines. Now turn the low tone way down and the high tone way up. Strum the same chords and play the same melodies, and really intently try to listen to the sound as if it were a landscape spread out before you. Try to "hear" the lack of lower frequencies; try to hear the increased presence of high frequencies. How would you describe the "terrain?" A lot of people would describe the sound as tinny, or at least fairly edgy. If you turn on some distortion in this setting it can have a particularly buzzsaw, grating quality. A lot of the Dead Kennedy's guitar sound involves this sort of high-frequency enhanced distortion.
Now go for the opposite: a lot of low tone, and very little high. Play the same chords and melodies. I wouldn't be surprised if the chords sound like mush in this environment. It's a sound that tends to be very muddy and almost "underwater." This isn't surprising since low frequencies travel through water, but high frequencies don't. Although the chords are probably unusably muddy in this environment, the melodies might have a cool, muted quality that works in low registers. Distortion in this soundworld is a relatively muted effect, because a lot of the sound of distortion lives in the higher frequencies.
You get the idea. Try cutting out only the mids and listen for a "hollow" character. Switch between the neck and bridge pickups; the former should be much mellower, tending to favor mids and lows, while the latter will be substantially more nasal and tinny, favoring the highs. If you have a wah pedal, play around with very slow movements of the pedal. As you open up the wah filter, listen for high frequencies emerging and as you close it, listen to how they're attenuated and your focus shifts to the muddier lows.
Build some strange "soundscapes" with your guitar, and try to predict what they will sound like—at least broadly—before you play any notes. The more you listen three dimensionally, the better you'll get at recognizing what's missing or overabundant in a variety of playing situations.
