Score coloration calculation

Started by xiando

xiando Lv 1

Score coloration

From what I gathered during a brief conversation in main chain, score colorations are a assigned by use of a ?linear? function based on three values, min energy, maximum energy, and the median energy value for the amino string.

One small problem I have with this is that when a maximum energy value deviates significantly from that of the median, the score coloration is weighted in favor of that segment and often produces a situation in which there are essentially only two colors; green and red, with red being the hotspot and green all else.

While this is an unquestionably effective tool for visually isolating "hot" regions, in many cases I find it difficult to determine the direction in which a "hot chain needs to be directed simply because it so dominates the coloration that there is little else in the way of indicators (distorted backbone as shown by its coloration) as to how the backbone is out of alignment, and therefore, how to "fix" it.

…And it remains in this top heavy condition until the hot spot has been remedied.

What would be better, imo is if any point greater than say a few standard deviations from the median be "tossed' when determining the base coloration…Any values exceeding the clipping threshold and based on this new "maximum", could be colored white or some similar color if you desire to retain the hotspot marker.

This would, imo, allow both "normal" backbone gradations to show trends in the chain while maintaining the ability to determine isolated, high-magnitude problem areas

axcho Lv 1

The classic backbone coloring should return soon. Hopefully that will help a little bit. If it's still an issue, let me know and I'll try making sense of what you suggested again. :p

xiando Lv 1

For what it's worth…

if I understood what you said in global chat one evening a few weeks ago, the current calculation appears to be a linear interpolation based on min, max and median values,

If the set of values used were, for instance

{0,1,4,3,7,6,1,0,3,9,6,62,4,36,4,3,6,5},

and ignoring significant place errors...

mean = 8.89, min = 0, max = 62

Thus, the interpolation would skew the coloration towards the two high values, via deviant maximum and median values, resulting in coloration showing primarily green (and perhaps light green), plus a pair of very angrily red residues. I based this conclusion on observed behavior in the program (before the last update). It behaved in exactly this way in that form, and "normal" colorations were absent until such time as the player significantly reduced the instability of the high valued chains.

If, however, the two "hotspot" values above were isolated, ie, tossed during calculation of the score coloration function, then the bulk of the points would have "normal" coloration....then iff values outside the coloration range were given a final color...say white, or light purple, or whatever, then both objectives would be met: normal energy gradations would show for all of the side chains, AND hotspots would be clearly identifiable from more "normal" maximums...viola...problem solved (coloration would no longer be skewed until the hotspots are dealt with), and useful feature gained, ie,hotspots can now be clearly delineated from high "normal" values...

{0,1,4,3,7,6,1,0,3,9,6,4,4,3,6,5} (toss, 62,36)
mean1 = 3.88, min1 = 0, max1 = 9
then If x> max1, Color(x) = ex:white, else Color(x) = f(x),
where f(x) represents the trimmed coloration function

--- If I'm not mistaken, the old method was similar to what I propose, except that the threshold is stated as "for all values EQUAL TO or above the median-based max, let color = bright red" ---

In mine, it would read "for all values above the median based max, a let color = (ex: white)
and the median would be calculated by first removing the "offending" points, themselves determined by a measure of either standard deviation or variance, whichever is computationally less intensive. this is where I suppose it gets tricky, but I hope you see where I'm going. In my ideal, the hotspots wouldn't be colored red, but they would have a value different from others, hence white, bright yellow, magenta, or something else deviating from the normal span

fwiw, I used such a technique to isolate mountainous terrain from "lowland" terrain in a color coding of a fractal surface generator many years ago, and while the requirements were slightly different, the global objective is identical...increased sensitivity in low magnitude areas and coalescence it in high magnitude areas. One could carry the idea even further, but it is probably sufficient for our need to simply delineate the hotspots from the high "normal" values by separating their colors by more than just a shade

In any case, I'm glad you reverted the color code for the interim, since I now have a better idea of what is and isn't in need of work Smile

xiando Lv 1

if the coloration is such that one cannot see trends in the energy
distribution, then one cannot easily fix the offending sidechain(s) so
coloration takes much longer and much more guesswork to come into focus
that it would otherwise do, which goes back to the original issue, and
one ends up guessing alot more than they need do