Fix for incorrect tick format in matrix & update disco scale

[creilly8]

Description

Addresses the ticks in this matrix example appearing in scientific notation. Several new units were added to verify the correct rendering for varying data range conditions.

Also addresses request to update the color direction and tick labels in the disco plot. Please use this example to test.

Checklist

Check each task that has been performed or verified to be not applicable.

• Tests: added and/or passed unit and integration tests, or N/A
• Todos: commented or documented, or N/A
• Notable Changes: updated release.txt, prefixed a commit message with "fix:" or "feat:", added to an internal tracking document, or N/A

[karishma-gangwani]

Hi @creilly8 in mbmeta, genome browser tab, search 'MYC', will load cnv segments atop the protein tk, when I increment the color scale +1 one at a time under the fixed option, from -2/+2 to -3/+3 the UI doesn't do anything except change the number of ticks from 4 to 3. the scale still remains at -2/2 and changing it to -4/+4 changes the scale. and if I go all the way upto -8/+8 it comes down to -5/+5. Should it have some sort of a lower/upper limit based on the actual cnv?

[creilly8]

Hi @creilly8 in mbmeta, genome browser tab, search 'MYC', will load cnv segments atop the protein tk, when I increment the color scale +1 one at a time under the fixed option, from -2/+2 to -3/+3 the UI doesn't do anything except change the number of ticks from 4 to 3. the scale still remains at -2/2 and changing it to -4/+4 changes the scale. and if I go all the way upto -8/+8 it comes down to -5/+5. Should it have some sort of a lower/upper limit based on the actual cnv?

Do you have a link?

[karishma-gangwani]

Hi @creilly8 in mbmeta, genome browser tab, search 'MYC', will load cnv segments atop the protein tk, when I increment the color scale +1 one at a time under the fixed option, from -2/+2 to -3/+3 the UI doesn't do anything except change the number of ticks from 4 to 3. the scale still remains at -2/2 and changing it to -4/+4 changes the scale. and if I go all the way upto -8/+8 it comes down to -5/+5. Should it have some sort of a lower/upper limit based on the actual cnv?

Do you have a link?

try this you will have to edit the scale and check though.

[creilly8]

Hi @creilly8 in mbmeta, genome browser tab, search 'MYC', will load cnv segments atop the protein tk, when I increment the color scale +1 one at a time under the fixed option, from -2/+2 to -3/+3 the UI doesn't do anything except change the number of ticks from 4 to 3. the scale still remains at -2/2 and changing it to -4/+4 changes the scale. and if I go all the way upto -8/+8 it comes down to -5/+5. Should it have some sort of a lower/upper limit based on the actual cnv?

Do you have a link?

@karishma-gangwani, I see the scale change the tick placement according to the overall range and the track reload. The placement of the ticks and the labels is dictated by d3. I'm not sure what you mean by lower and upper limit. If it's input validation, then the caller needs to validate the input. The color scale wouldn't know what would be the absolute max and min values for the track.

[karishma-gangwani]

also, in the matrix link you shared the scale numbers seem shifted for the gain. can you check?

[creilly8]

also, in the matrix link you shared the scale numbers seem shifted for the gain. can you check?

The scale uses the actual max value instead of 1. That's why 1 appears to the left.

[karishma-gangwani]

also in copy number loss, shouldn't the darker blue represent a higher magnitude of the loss? so the scale should be reverse for that one. -1 -2 representing heterozygous, homozygous deletion should be on the darker end and not the lighter
@xzhou82 can you confirm?

This is fixed in 7bf03cd.

[karishma-gangwani]

also in copy number loss, shouldn't the darker blue represent a higher magnitude of the loss? so the scale should be reverse for that one. -1 -2 representing heterozygous, homozygous deletion should be on the darker end and not the lighter @xzhou82 can you confirm?

This is fixed in 7bf03cd.

Thanks! Looks good

[xzhou82]

Do not use if either value is 0 is not valid. e.g. range is from 0 to 100000. still want scientific

[creilly8]

What's the cutoff? When the range between the min and max is >=10 use scientific notation? or 100? or 1000?