fixing rounding issue in min-max slider

[evelyn-schmidt]

@mhoang22 encountered a problem where the dynamic scatter doesn't show all candidates for the custom module. In her pvacsplice output, there were 5 candidate groups (corresponding to 5 genes associated with the neoantigens). She expected to see 5 dots corresponding to the 5 candidate groups. However, only saw 3 candidates. When examining the ‘Overview of Neoantigen Features’ board again, it looks like the 2 candidate groups with extreme VAF values (1st candidate: gene ATG12: tumor DNA VAF 0.432 , tumor RNA VAF 0.387; 5th candidate: gene TP53: tumor DNA VAF 0.852, tumor RNA VAF 0.998) are the missing candidates. If she natural-logged transformed both x and y axis, then she could see 5 candidates. She concluded that there was a reason that candidates with edge values were being excluded.

I found that these edge cases were being missed because of the rounding that happens to create the min-max slider. The range used for the min-max slider was originally rounded and now is just set as the dataset min/max.

pVACtools/pvactools/tools/pvacview/server.R

Lines 2120 to 2121 in efc101f

	min_value <- as.numeric(format(round(range_values[1], 2), nsmall = 2))
	max_value <- as.numeric(format(round(range_values[2], 2), nsmall = 2))

So the change looks like this:

pVACtools/pvactools/tools/pvacview/server.R

Lines 2117 to 2118 in ef27b63

	min_value <- round(range_values[1], 10)
	max_value <- round(range_values[2], 10)

[susannasiebert]

We could also consider using floor and ceiling in order to round down (for the min_value) and up (for the max_value), respectively. Not sure if, for display purposes, an int number is preferred, e.g. if the min_value and max_value are displayed on the chart axes and sliders.

[evelyn-schmidt]

Yeah, @susannasiebert , I like the floor/ceiling suggestion because it looks a little cleaner on the slider.

However, is the most clear option for users to set the max/min value to the actual min/max value in the dataset? So you can see the maximum and minimum values on the slider?

[susannasiebert]

I personally don't think they need to match. They can always retrieve the actual min max value by hovering over the appropriate datapoint, right?

[ldhtnp]

Everything looks good to me. I agree with using floor and ceiling to have cleaner values displayed on the slider. I provided suggestions to add this