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statonlab / hardwoods_site

Hardwoods Genomics bugs, data loading, and general issues
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Expression Bar Charts in F. sylvatica #546

Open MattHuff opened 4 years ago

MattHuff commented 4 years ago

Bug description

This is related to #542 - Fagus Sylvatica. While I have confirmed that the Treatments on the Biological Samples have been updated, when I pull up a gene's Expression bar chart, it is still shows that a vast majority of samples are marked as "Not Set," and "Drought" appears twice as a treatment:

https://hardwoodgenomics.org/feature/FSB012355501?tripal_pane=group_expression https://hardwoodgenomics.org/feature/FSB010968101?tripal_pane=group_expression

Additionally, despite being set at "Treatment" by default, that is not the correct bar chart for "Treatment." To get the correct bar chart, I must manually switch to a different property, and then switch back.

almasaeed2010 commented 4 years ago

Let's re-populate the materialzed view to see if that updates the charts.

I'll also look into the code that sets the property

almasaeed2010 commented 4 years ago

The property dropdown issue has been fixed.

Repopulating the materialized view doesn't seem to have done the trick though. I'll verify the data is correct in Chado to make sure manual changes are taking effect.

almasaeed2010 commented 4 years ago

Looks like the loader is getting data from chado directly. How did you add the expression data? Can you point me to the documentation you used or describe the process please?

MattHuff commented 4 years ago

@RaymondS1 loaded the expression data.

Last night, I looked at a random gene found using the Feature Search tool, and aside from Drought appearing as a condition twice, it has correctly updated the Treatments so only one sample is "Not Set:"

https://hardwoodgenomics.org/feature/FSB014161301?tripal_pane=group_expression

However, the genes that I am interested in, which Ray determined to be the most differentially expressed genes using DESeq2, still have the issue with most samples appearing as "Not Set." This would appear to be an issue with my caching, and not with the website itself.