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Antibody summary display #136

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Bernadetadad opened this issue Dec 19, 2024 · 2 comments · Fixed by #137
Closed

Antibody summary display #136

Bernadetadad opened this issue Dec 19, 2024 · 2 comments · Fixed by #137
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@jbloom

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@Bernadetadad
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The current faceted summary view of antibodies from VRC has a couple issues:

  • I don't think it should have mean antibody escape for all antibodies at the top, I'm not sure that gives any useful information
  • There needs to be more spacing between the facets because antibody names do not fit (or maybe antibody names should be displayed vertically)
  • I did include no_heatmap: True setting for the antibodies because I think the sliders are sufficient in this case and heatmaps just clutter things but for some reason heatmaps are still being displayed (probably overwritten by phenotypes params), I'm not sure how to fix this
@jbloom
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jbloom commented Dec 20, 2024

@Bernadetadad Are you sure you get heatmaps if you put no_heatmap both for the antibodies and each phenotype? When I do that I don't see any heatmaps. Note you need to put no_heatmap: true under each antibody set, not as a top-level key for antibody_escape.

I am working on the other things still.

jbloom added a commit to dms-vep/dms-vep-pipeline-3 that referenced this issue Dec 20, 2024
@jbloom
Add option no_mean_lineplot to summaries to not show antibody-escap…
0d4241d 
…e mean lineplot (see [this issue](dms-vep/Flu_H5_American-Wigeon_South-Carolina_2021-H5N1_DMS#136))
jbloom added a commit to dms-vep/dms-vep-pipeline-3 that referenced this issue Dec 20, 2024
@jbloom
Add option lineplot_antibody_label_loc ("right" or "top") for label…
a3f0894 
…s on antibody-escape lineplots ((see [this issue](dms-vep/Flu_H5_American-Wigeon_South-Carolina_2021-H5N1_DMS#136)).
@Bernadetadad
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Ah, I only put it under the antibodies.

@jbloom jbloom mentioned this issue Dec 28, 2024
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jbloom added a commit to dms-vep/dms-vep-pipeline-3 that referenced this issue Dec 29, 2024
@jbloom
make a variety of improvements to the summary plots (#178)
680b7ce 
* add example summary plot w no heatmaps or antibody-escape mean

* Add option `no_mean_lineplot` to summaries to not show antibody-escape mean lineplot (see [this issue](dms-vep/Flu_H5_American-Wigeon_South-Carolina_2021-H5N1_DMS#136))

* Add option `lineplot_antibody_label_loc` ("right" or "top") for labels on antibody-escape lineplots ((see [this issue](dms-vep/Flu_H5_American-Wigeon_South-Carolina_2021-H5N1_DMS#136)).

* make `no_mean_lineplot` global `antibody_escape` option and recolor facet plots accordingly

* add line plot site labels when only one antibody per group (addresses #177)

* add `scale_lineplot_height` option

* some streamlining of summary notebook plotting

* add `per_antibody_selectable_heatmap` option

* `black` formatting

* re-run pipeline
@jbloom jbloom mentioned this issue Dec 29, 2024
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@jbloom jbloom linked a pull request Dec 29, 2024 that will close this issue
improved formatting of VRC antibodies summary plot #137
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