search

maximilianh / cellBrowser

main repo: https://github.com/ucscGenomeBrowser/cellBrowser/ - Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org
https://github.com/ucscGenomeBrowser/cellBrowser/
GNU General Public License v3.0
104 stars 40 forks source link

Gene box functionality #3

Closed hbeale closed 6 years ago

hbeale commented 6 years ago

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 commented 6 years ago

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 notifications@github.com 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 https://github.com/maximilianh/cellBrowser/issues/3, or mute the thread https://github.com/notifications/unsubscribe-auth/AAS-TSjtJAFbEppvR9a4bDZ90IGve1jPks5srpgzgaJpZM4P3vZe .

hbeale commented 6 years ago

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:

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 notifications@github.com 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 https://github.com/maximilianh/cellBrowser/issues/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 https://github.com/maximilianh/cellBrowser/issues/3#issuecomment-336304778, or mute the thread https://github.com/notifications/unsubscribe-auth/AADVg_HPO_3pwCn5hNseIp4y-su9ZLGYks5srptCgaJpZM4P3vZe .

maximilianh commented 6 years ago

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 notifications@github.com 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 < notifications@github.com> 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 notifications@github.com 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 https://github.com/maximilianh/cellBrowser/issues/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 https://github.com/maximilianh/cellBrowser/issues/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 https://github.com/maximilianh/cellBrowser/issues/3#issuecomment-336305490, or mute the thread https://github.com/notifications/unsubscribe-auth/AAS-TYmuCD2CJqsYaU8TXHmNUz2Ct96kks5srpv_gaJpZM4P3vZe .

maximilianh commented 6 years ago

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

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 notifications@github.com 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 < notifications@github.com> 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 notifications@github.com 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 https://github.com/maximilianh/cellBrowser/issues/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 https://github.com/maximilianh/cellBrowser/issues/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 https://github.com/maximilianh/cellBrowser/issues/3#issuecomment-336305490, or mute the thread https://github.com/notifications/unsubscribe-auth/AAS-TYmuCD2CJqsYaU8TXHmNUz2Ct96kks5srpv_gaJpZM4P3vZe .