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MD-Anderson-Bioinformatics / NG-CHM

A dynamic, graphical environment for exploration of clustered or non-clustered heat map data in a web browser.
https://bioinformatics.mdanderson.org/main/NG-CHM-V2:Overview
GNU General Public License v2.0
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PT #165456012 Dendrogram selections not working properly. #125

Open jmelott opened 3 years ago

jmelott commented 3 years ago

Originally Pivotal Tracker issue: https://www.pivotaltracker.com/story/show/165456012 bug entered by James M. Melott on 04/18/2019

Multiple step dendrogram selections and deselections leaves selected area different from what should be selected and what dendrogram highlighting displays as selected. Tested on multiple TCGA maps. Steps to repeat: 1) Pick map like http://tcga.ngchm.net/NGCHM/chm.html?map=38f7f656d4df587448f64ff882de4d212d3e713c 2) Select 4 multiple lower level consecutive dendrogram areas that are about the same level in the dendrogram. 3) Deselect 3rd selected area. 4) Deselect 2nd selected area. 5) Reselect 2nd area. (At this point all 4 areas are probably selected) 6) Deselect 2nd area again.

Would expect map to have only 1st and 4th areas on dendrogram highlighted and only areas under those selected. Instead, 1st and 4th correctly highlighted on dendrogram but selected area on map also includes 3rd area. (See attached image)

dendrogram_selection_issue

jmelott commented 3 years ago

@markstucky - May 15 2019, 3:59 pm I tried several times to reproduce this using the same map (in Chrome and Firefox) that was listed above from tcga.ngchm.net. Select 4 contiguous; deselect 3; deselect2; re-select 2; deselect 2. In each case only 1 and 4 were highlighted and selected. I see the picture attached to this item, but could not reproduce the results.

Dendro clicking can be tricky at lower levels and this scenario may possibly occur but, if it happens only rarely on a scenario that is uncommon, I think we'd be okay not further investigating this.

@markstucky - May 15 2019, 5:31 pm This is another one where, should we decide to work on it, it would be better to wait until Bradleys dendro performance logic is implemented.

@markstucky - Jul 11 2019, 8:06 am Could not reproduce after new dendrogram pull request implemented. Re-test on version 2.10.

@markstucky - Jul 11 2019, 9:04 am Code checked-in

jmelott commented 3 years ago

@jamesm5 - Aug 8 2019, 10:24 am Still some confusing issues with this.

Basic issue: it is very easy, clicking, ctrl-clicking, and/or shift-clicking in just the dendrograms areas to get the selected labels/map areas and the highlighted dendrogram areas out-of-sync with each other.

Using map from vor http://vor.mdanderson.edu:9911/NGCHM/chm.html?map=4e8c2a9de1aff1d18eace5cf87b22358856a3c55 which is tcga_rppa_cesc_v2.0_sample_sample.

Mainly tested with upper dendrogram. Left dendrograms have similar issues, but possibly seem to work a little more reliably than the upper dendrogram.

If click on one dendrogram area and then shift-click on on some other one, all the labels between those two clicks are selected, but only the two dendrogram areas directly clicked on are highlighted in the dendrogram area. If then ctrl-click on any line in the dendrogram area that is part of the selected labels, the first ctrl-click usually acts like a select, and marks the clicked area of the dendrogram as selected (the labels reman selected). Then pressing ctrl-click on the same spot sometimes deselects the dendrogram area, and sometimes doesn't. I haven't been able to figure out a consistent pattern of when it does or doesn't work.

@jamesm5 - Aug 8 2019, 10:25 am Easy to get selected dendrogram areas and selected map labels/map areas out of sync.

@markstucky - Aug 8 2019, 10:25 am Hi James, Has this one been retested since you got the latest version for testing late last Thursday? The last update is from before that time. Can you please verify that this has failed in a retest? Thanks.

jmelott commented 3 years ago

@jamesm5 - Aug 19 2019, 9:56 am Hi Mark, Yes, it is still happening. It is very repeatable. I retested this morning on both Chrome and Firefox and it works the same way on both, so it doesn't seem to be a browser-specific issue.

I've created a more detailed capture of the steps below so you can try to reproduce the issue on your side. See attached bmp image and map.

Numbers below match numbered steps in attached bmp. Open map. Selections listed below made by clicking on the horizontal bars in the upper dendrogram area. 1) Select first dendrogram area. 2) Shift-select second area. 3) Shift-select third area. 4) Shift-select fourth area. 5) Shift-deselect third area. 6) Shift-deselect forth area. (All working as expected so far) 7) Shift-select second area. (Third area cells also get selected even though they shouldn't be, but third dendrogram area not selected) 8) Shift-deselect second area (Issue with third area still exists)

I also got the same behavior using the next higher levels of horizontal dendrogram bars. Dendro_issues_sequence

tcga_rppa_cesc_v2.0_sample_sample.ngchm.zip

jmelott commented 3 years ago

@markstucky - Aug 19 2019, 10:29 am Thanks James. I had to check because there was no indication of a retest after the discovery that the previous rejection took place on the wrong version of the software. Can you retest the other 2 items that are in a rejection state (#166823171 and #165476233) ,which were also rejected on an outdated version of the software?

jmelott commented 2 years ago

Still present 2022 02 07.