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error saving curated volin plot #875
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also happening for dataset: for both these datsets i have static umap plots create no prob |
What conditions are you trying to plot? |
expression on Y-axis, "dev_state" on the X-axis - everything else is default settings i all cases, im now getting this error instead of the original one i sent "Something went wrong. Please contact the gEAR team and provide steps to reproduce." |
in addition to the different error now, i am not evne getting to the screen where i sent the screen cap above - it gives the erros right when i hit the plot button |
Actually getting a chance to look at this. It's a Javascript error related to a warning that is supposed to show in addition when a data series (in this case "dev_state") has too many groups that could result in a crowded plot. Going to work on fixing this warning |
Cool
…On Wed, Sep 4, 2024, 13:51 Shaun Adkins ***@***.***> wrote:
Actually getting a chance to look at this. It's a Javascript error related
to a warning that is supposed to show when a data series (in this case
"dev_state") has too many groups that could result in a crowded plot. Going
to work on fixing this warning
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Works now. Closing |
Awesome- thnx!
…On Wed, Sep 4, 2024, 14:36 Shaun Adkins ***@***.***> wrote:
Closed #875 <#875> as completed.
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sorry shaun - still having issues. when i try this: https://nemoanalytics.org/dataset_curator.html?dataset_id=6b3f05b3-0885-4765-8d6b-c449753823b6 or this https://nemoanalytics.org/dataset_curator.html?dataset_id=1cac4125-7083-4754-9aa6-6964c8d9ffec and then enter violin plot details i get an eternally loading symbol when i hit the PLOT button: |
Seems it's a separate issue with rendering the group series "sortable" component that lets you reorder facets, legends, etc. Pretty sure it's because the "stage.ord" series name has a period in it, which the HTML Sortable component does not like. However, it seems that the groups of sortable lists rendered does not reflect the chosen groups for the plot either (containing more groups than were specified) |
Ok fixed the issue where the plot will now render (forgot to escape a CSS selector ID). However I still need to work on the issue where old sortable series not currently applicable need to be removed. |
Closing ticket as things seem to be in working order now. I also resolved the issue from the previously mentioned comment |
Thnx shaun!
…On Fri, Sep 6, 2024, 10:10 Shaun Adkins ***@***.***> wrote:
Closed #875 <#875> as completed.
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hey shaun - i was able to make a violin plot for both of the datasets, using the "stage.ord" meta data column, but when i try it with "dev_state" i am still getting this error for both datasets: "Could not create Plotly plot for this dataset and parameters. Please contact the gEAR team." |
Fixed some issues in #827 that may (or may not) also resolve your issues @carlocolantuoni |
Cool, thnx, i ll giv it a try again
…On Mon, Sep 9, 2024, 10:38 Shaun Adkins ***@***.***> wrote:
Fixed some issues in #827 <#827> that
may (or may not) also resolve your issues @carlocolantuoni
<https://github.com/carlocolantuoni>
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@carlocolantuoni are the issues still persisting? |
ya there are still when i try to make a violin plot for super weird as it looks exactly like what you are doing without error |
but if i plot and color by "dev_state" it fails with that error. |
I'd like to get it working though, so I'll tackle that after #886. There's a good chance others would encounter a similar issue under the same conditions (but different dataset and configuration). Thanks for the update. |
thnx shaun
…On Mon, Sep 16, 2024 at 11:56 AM Shaun Adkins ***@***.***> wrote:
I'd like to get it working though, so I'll tackle that after #886
<#886>. There's a good chance others
would encounter a similar issue under the same conditions (but different
dataset and configuration). Thanks for the update.
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Carlo
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Seems the issue is that there there is a missing value (nan) present in the color mapping which is causing type incompatibilities. I believe this is because the "NA" present as a "dev_state" category is being converted to "nan" (the pandas missing value indicator). Reference -> https://stackoverflow.com/questions/33952142/prevent-pandas-from-interpreting-na-as-nan-in-a-string |
Unfortunately it seems like the AnnData reader has no way to remove "NA" as a default missing value, so it automatically gets converted into NaN. Normally I'd just say "ok, let's just turn them back into NA again", but I'm worried about edge cases where someone had both "NA" and missing values in a metadata category and then we may be incorrectly merging two bad properties. Honestly though, if that ever becomes an issue, I would attribute it to being a terrible dataset. So I think I'm going to try and catch these missing values, and unify them if I can, at least to whatever is found in the color mapping. |
I pushed a fix that makes it work. However, the NA column does not show in the plot, but at least it is not erroring for me now. |
👍👍
…On Mon, Sep 16, 2024 at 3:38 PM Shaun Adkins ***@***.***> wrote:
I pushed a fix that makes it work. However, the NA column does not show in
the plot, but at least it is not erroring for me now.
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@carlocolantuoni I am closing this in favor of #888, since the issue is more focused now. |
👍
…On Tue, Sep 17, 2024, 08:43 Shaun Adkins ***@***.***> wrote:
@carlocolantuoni <https://github.com/carlocolantuoni> I am closing this
in favor of #888 <#888>, since the
issue is more focused now.
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hi guys,
im getting "Could not create Plotly plot for this dataset and parameters. Please contact the gEAR team."
when trying to save a violin plot for the following dataset
dataset_id=6b3f05b3-0885-4765-8d6b-c449753823b6
The text was updated successfully, but these errors were encountered: