Gene box functionality

[hbeale]

When we view our data with the browser, the gene boxes are less functional that with the test data. The boxes don't dynamically change color based on the circle selected.

[maximilianh]

This is a bug and I've been looking into it for a while today. The source of the problem is that your marker list has genes in it that are not in your matrix e.g. AKT1. I wonder how this can happen...

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On Thu, Oct 12, 2017 at 3:52 PM, hbeale ***@***.***> wrote: When we view our data with the browser, the gene boxes are less functional that with the test data. The boxes don't dynamically change color based on the circle selected. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#3>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAS-TSjtJAFbEppvR9a4bDZ90IGve1jPks5srpgzgaJpZM4P3vZe> .

[hbeale]

Well, that’s a problem we should be able to fix on our end. Limiting the marker list to genes in the matrix seems like a reasonable requirement. Thanks!! On Thu, Oct 12, 2017 at 4:05 PM Maximilian Haeussler < notifications@github.com> wrote:

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This is a bug and I've been looking into it for a while today. The source of the problem is that your marker list has genes in it that are not in your matrix e.g. AKT1. I wonder how this can happen... On Thu, Oct 12, 2017 at 3:52 PM, hbeale ***@***.***> wrote: > When we view our data with the browser, the gene boxes are less functional > that with the test data. The boxes don't dynamically change color based on > the circle selected. > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#3>, or mute the thread > < https://github.com/notifications/unsubscribe-auth/AAS-TSjtJAFbEppvR9a4bDZ90IGve1jPks5srpgzgaJpZM4P3vZe > > . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#3 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AADVg_HPO_3pwCn5hNseIp4y-su9ZLGYks5srptCgaJpZM4P3vZe> .

[maximilianh]

I've fixed this now in the viewer on http://hgwdev-max.soe.ucsc.edu/tsneViewer/dev3/ and am working through the code to fix it in the prep script. You can also multi select different legend items now.

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On Thu, Oct 12, 2017 at 4:08 PM, hbeale ***@***.***> wrote: Well, that’s a problem we should be able to fix on our end. Limiting the marker list to genes in the matrix seems like a reasonable requirement. Thanks!! On Thu, Oct 12, 2017 at 4:05 PM Maximilian Haeussler < ***@***.***> wrote: > This is a bug and I've been looking into it for a while today. The source > of the problem is that your marker list has genes in it that are not in > your matrix e.g. AKT1. I wonder how this can happen... > > On Thu, Oct 12, 2017 at 3:52 PM, hbeale ***@***.***> wrote: > > > When we view our data with the browser, the gene boxes are less > functional > > that with the test data. The boxes don't dynamically change color based > on > > the circle selected. > > > > — > > You are receiving this because you are subscribed to this thread. > > Reply to this email directly, view it on GitHub > > <#3>, or mute the > thread > > < > https://github.com/notifications/unsubscribe-auth/AAS- TSjtJAFbEppvR9a4bDZ90IGve1jPks5srpgzgaJpZM4P3vZe > > > > . > > > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#3 (comment)- 336304778>, > or mute the thread > <https://github.com/notifications/unsubscribe- auth/AADVg_HPO_3pwCn5hNseIp4y-su9ZLGYks5srptCgaJpZM4P3vZe> > . > — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#3 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAS-TYmuCD2CJqsYaU8TXHmNUz2Ct96kks5srpv_gaJpZM4P3vZe> .

[maximilianh]

cbPrep now outputs: gene AKT1 in the default gene list (option -g) is not in the expression matrix. " "It will be skipped now and will not appear in the gene list I think these two fixes should make this problem go away from now on. On Thu, Oct 12, 2017 at 4:31 PM, Maximilian Haeussler <maximilianh@gmail.com

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wrote: I've fixed this now in the viewer on http://hgwdev-max.soe.ucsc. edu/tsneViewer/dev3/ and am working through the code to fix it in the prep script. You can also multi select different legend items now. On Thu, Oct 12, 2017 at 4:08 PM, hbeale ***@***.***> wrote: > Well, that’s a problem we should be able to fix on our end. Limiting the > marker list to genes in the matrix seems like a reasonable requirement. > > Thanks!! > > On Thu, Oct 12, 2017 at 4:05 PM Maximilian Haeussler < > ***@***.***> wrote: > > > This is a bug and I've been looking into it for a while today. The > source > > of the problem is that your marker list has genes in it that are not in > > your matrix e.g. AKT1. I wonder how this can happen... > > > > On Thu, Oct 12, 2017 at 3:52 PM, hbeale ***@***.***> > wrote: > > > > > When we view our data with the browser, the gene boxes are less > > functional > > > that with the test data. The boxes don't dynamically change color > based > > on > > > the circle selected. > > > > > > — > > > You are receiving this because you are subscribed to this thread. > > > Reply to this email directly, view it on GitHub > > > <#3>, or mute the > > thread > > > < > > https://github.com/notifications/unsubscribe-auth/AAS-TSjtJA > FbEppvR9a4bDZ90IGve1jPks5srpgzgaJpZM4P3vZe > > > > > > . > > > > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on GitHub > > <#3# > issuecomment-336304778>, > > or mute the thread > > <https://github.com/notifications/unsubscribe-auth/AADVg_ > HPO_3pwCn5hNseIp4y-su9ZLGYks5srptCgaJpZM4P3vZe> > > . > > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#3 (comment)>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AAS-TYmuCD2CJqsYaU8TXHmNUz2Ct96kks5srpv_gaJpZM4P3vZe> > . >