pVACview reviewer response #1062

evelyn-schmidt · 2024-02-06T23:54:16Z

To add ease of use to pVACview, @huiming and I have created two new modules that can be used with input files from other neoantigen annotation tools. This includes a module for the popular tool NeoFox and a module called 'Custom' as it is meant to handle any neoantigen tool data. The new modules are implemented in the same server.R file as the base pVACview module but have separate ui.R.

NeoFox Module:

Custom:

…development)

…ithlab/pVACtools into pvacview_reviewer_response

…tarting selections, and add way for user to transform data

susannasiebert

This looks good to me with some minor issues as noted in separate comments.

I assume we can't split out the server.R file into separate modules? It would be nice if it could be split out by pvacseq/neofox/custom input to organize things a bit more.

susannasiebert · 2024-02-09T18:55:40Z

pvactools/tools/pvacview/run.py

@@ -16,7 +16,7 @@ def define_parser():
 def main(args_input = sys.argv[1:]):
    parser = define_parser()
    args = parser.parse_args(args_input)
-    arguments = ['{}'.format(args.r_path), "-e", "shiny::runApp('{}', port=3333)".format(args.pvacseq_dir)]


Was there a reason for this change? We need a consistent port in order for the deployed version to work.

susannasiebert · 2024-02-09T18:56:24Z

pvactools/tools/pvacview/__init__.py

@@ -1,5 +0,0 @@
-__all__ = [


I think we need to put this file back or the pvacview run command won't work correctly.

…r pvacview run command

…VACtools into pvacview_reviewer_response

…sing the error session(unbind-DT, mainTable)

…re generated from

…names does not break pvacview

…ts), and change names of a couple screenshots

susannasiebert

Finished review of the pVACview vignette in particular. I found a few typos and issues that lead to warnings when building the docs (title underlines too short; missing empty line after lists). I also expanded on a few explanations in the vignette where I felt more clarification could be useful.

docs/pvacview/pvacseq_module/pvacseq_vignette.rst

susannasiebert · 2024-04-29T20:02:32Z

docs/pvacview/prerequisites.rst

I believe that there are additional R packages needed for the new modules. Can you please add them to the installation instruction?

Co-authored-by: Susanna Kiwala <susanna.kiwala@wustl.edu>

…m Malachi and Susanna)

…into subsections

Co-authored-by: mhoang22 <98837430+mhoang22@users.noreply.github.com>

…edits Reviewing PR #1062

huimingx and others added 5 commits November 8, 2023 11:31

Add current version of pvacview files with additional modules (under …

69af1ac

…development)

Merge branch 'pvacview_reviewer_response' of https://github.com/griff…

9d74f05

…ithlab/pVACtools into pvacview_reviewer_response

Evelyn's edits to the code

1e1e191

workign neofox module, need to fix table next button, choose better s…

cee8241

…tarting selections, and add way for user to transform data

corrext vaxrank data

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evelyn-schmidt marked this pull request as ready for review February 6, 2024 23:56

susannasiebert changed the base branch from master to staging February 8, 2024 18:56

Evelyn Schmidt added 2 commits February 8, 2024 14:48

pvacview extra modules added

fda31e3

changed color from purple to the pvacview color

6ad31a5

susannasiebert force-pushed the pvacview_reviewer_response branch from c07d9d3 to 6ad31a5 Compare February 8, 2024 20:51

susannasiebert requested changes Feb 9, 2024

View reviewed changes

Evelyn Schmidt and others added 19 commits February 20, 2024 10:43

fixed run.py to include consistent port number and added init file fo…

c4bd9ca

…r pvacview run command

beginning of documentation update and some slight UI fixes to pvacview

f989a84

neofox documentation updates

ccacf61

resolve merge conflicts with pvacview v4.1.0

f0ec2b6

readthedocs documentation updates for neofox and custom modules

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update to the tutorial tab with new module information

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add screenshots and vignette

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adding sirt by and group by labels

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Merge branch 'pvacview_reviewer_response' of github.com:griffithlab/p…

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…VACtools into pvacview_reviewer_response

fixes

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modify vignette and add a screenshot folder for the vignette

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documentation edits

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Merge branch 'pvacview_reviewer_response' of github.com:griffithlab/p…

c71fe4a

…VACtools into pvacview_reviewer_response

fixing merge conflicts with staging

0fe7d88

update vignette

34be7a7

trying to fix overlapping servers

ae7ef4d

fixed modules overlapping each other -- this command seemed to be cau…

6d19b10

…sing the error session(unbind-DT, mainTable)

changed names of example data files to be more clear what tool they a…

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…re generated from

making sure that uploading a file to neofox without the right column …

faf361a

…names does not break pvacview

Evelyn Schmidt and others added 7 commits April 19, 2024 09:24

fix hover information incorrect alignment

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modify vignette. add more explanation about the Parameters

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fix bullet points

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minor edits

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add rda file for HCC1395 demo data

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add progress bar for demo data load; use rda to load demo data faster

d89d305

edit vignette (add to Example 2 ~ variant with multiple transcript se…

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…ts), and change names of a couple screenshots

susannasiebert requested changes Apr 29, 2024

View reviewed changes

susannasiebert reviewed Apr 29, 2024

View reviewed changes

mhoang22 and others added 20 commits May 2, 2024 23:59

Apply suggestions from code review

afaf009

Co-authored-by: Susanna Kiwala <susanna.kiwala@wustl.edu>

Apply suggestions from code review

61fd33d

Co-authored-by: Susanna Kiwala <susanna.kiwala@wustl.edu>

Apply suggestions from code review

8d3ac09

Co-authored-by: Susanna Kiwala <susanna.kiwala@wustl.edu>

incorporate suggesstions from Chris Miller (on top of suggestions fro…

1934b6b

…m Malachi and Susanna)

minor edits to vignette: split explanation of the tiering parameters …

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…into subsections

change name of figure from %ilePlot.png to percentilePlot.png

c76bb9e

edit vignette

e782ddb

removing testing files which are no longer needed

e510512

deleting .Rhistory

9babb20

Re-review pVACview vignette

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Review custom pVACview module documentation

70bbd4e

Review NeoFox pVACview module documentation

1e562fb

Update tutorial formatting

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Add clarifying text for custom module demo data loading

c52b043

Add installation instructions for new R dependencies

b272dad

Move Tutorial further down in the sidebar menu

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Remove unneeded file

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More typo and grammar fixes

c0ef503

Apply suggestions from code review

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Co-authored-by: mhoang22 <98837430+mhoang22@users.noreply.github.com>

Merge pull request #1100 from griffithlab/pvacview_reviewer_response_…

3b53aa2

…edits Reviewing PR #1062

susannasiebert merged commit f8add9d into staging May 8, 2024
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pVACview reviewer response #1062

pVACview reviewer response #1062

evelyn-schmidt commented Feb 6, 2024

susannasiebert left a comment

susannasiebert Feb 9, 2024

susannasiebert Feb 9, 2024

susannasiebert left a comment

susannasiebert Apr 29, 2024

pVACview reviewer response #1062

pVACview reviewer response #1062

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