Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Draw variants transcript and protein #148

Merged
merged 63 commits into from
Apr 23, 2024
Merged

Draw variants transcript and protein #148

merged 63 commits into from
Apr 23, 2024

Conversation

pnrobinson
Copy link
Collaborator

No description provided.

frehburg and others added 30 commits December 22, 2023 15:26
@frehburg
added rough sketch of figure in notebook
821078a
@ielis
Add visualization prose.
9fcfd1f
@frehburg
Merge pull request #125 from monarch-initiative/visualization-prose
6225ae2 
Add visualization prose
@frehburg
created new file for VariantVisualizer and moved basic drawing methods
4389c6d
@frehburg
moved drawing code from notebook to class
0ea61ea
@frehburg
helper methods private
0a98f97
@frehburg
added constructor to load all necessary information
aa6aae0
@frehburg
extracted colors of markers, exons and gray bar to constructor
18c529f
@frehburg
renamed the 'gray bar' to 'protein_track'
d684ca2
@frehburg
moved color of axes to constructor self.axis_color
a7f2678
@frehburg
moved exon outliune color and corrected bug
5c8b843
@frehburg
also moved colors of features
715ae91
@frehburg
included cycle for color of exons
89a6288
@frehburg
renamed outline variables to outline_color for clarity
bfccd3c
@frehburg
moved notebook to facilitate execution (correct path references)
bc62cdb
@frehburg
changed colors
76cffe6
@frehburg
removed unused imports
0f55cab
@frehburg
renamed location variables to correct terminology
01192b2
@frehburg
added title to include the transcript id, protein id, protein name
7123c0a
@frehburg
corrected terms in comments
8180cb9
@frehburg
clarified comments more
f40c65f
@frehburg
renamed variables to increase readability
e8e8817
@frehburg
corrected wrong variable name
1ae028c
@frehburg
rewrote exon plotting to work on provided transcript data
89e6268
@frehburg
changed some numbers for more accurate representation
4966a69
@frehburg
fixed bug in visualization, now lower track displayed correctly
649dfbd
@frehburg
added exon label field to variantvisualizer
77e8f10
@frehburg
changing features to real data, currently not working due to codon in…
3adf5f2 
…dexing
@frehburg
git issue
0af5b2c
@frehburg
added todo for method signature
114773d 
Signed-off-by: frehburg <fil.rehburg@gmail.com>
frehburg and others added 23 commits February 21, 2024 12:52
@frehburg
fixed bug: method didn't return anything
df19292
@frehburg
updated nb to include state info
bdd9954
@frehburg
typo: missing s
68c8db3
@frehburg
remved unnecessary ()
5a163f7
@frehburg
assigning colors to each marker
9789ae4
@frehburg
converting from codons to bases as indices
ae0b114
@frehburg
changed drawing of markers to center between start and finish
9411d68
@frehburg
made feature colors deterministic and cycle through them
dac3841 
Signed-off-by: frehburg <fil.rehburg@gmail.com>
@frehburg
added names and colors for each feature type
277f91f
@frehburg
refactoring
931eb64
@frehburg
assembling info about features
0cfd96e
@frehburg
refactoring in marker drawing
23e8c4d
@frehburg
refactoring in feature drawing to incorporate new info
b08893d
@frehburg
added label with name of feature
8840605
@frehburg
figure working
a2b4a12 
Signed-off-by: frehburg <fil.rehburg@gmail.com>
@frehburg
added track similar to protein for transcript
0fea668
@frehburg
changed draw marker method to prevent stem overlap with circle
b736d97
@frehburg
refactoring for clarity
018087a
@frehburg
renamed transcript_... to exon_...
452d799
@frehburg
added labels to exons
ad096e5
@frehburg
added todo for legend, renamed exon in one place
4fdf3b6
@pnrobinson
Merge branch 'refs/heads/develop' into draw-variants-transcript-and-p…
a564264 
…rotein
@pnrobinson
test vv response
77171e6
@pnrobinson
Copy link
Collaborator Author

@ielis @lnrekerle
This PR adds the drawing code as well as a test case for the VariantValidator response. The function, parse_response, line 157 of _vv.py, will also need to be changed -- to me it looks as if the code is expecting a different JSON structure from what we actually get -- I added the test case to understand the structure. Unless there is some other code that only passes part of the response, it is wrong
PLEASE ADD DOCUMENTATION TO ALL FUNCTIONS LIKE THIS! It would be a lot easier to contribute code if the main assumptions and goals of each function were documented --

lnrekerle
lnrekerle approved these changes Apr 23, 2024
View reviewed changes
Copy link
Collaborator

@lnrekerle lnrekerle left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This looks good to me!

@lnrekerle
Copy link
Collaborator

lnrekerle commented Apr 23, 2024 •
edited
Loading

The function, parse_response, line 157 of _vv.py, will also need to be changed -- to me it looks as if the code is expecting a different JSON structure from what we actually get -- I added the test case to understand the structure. Unless there is some other code that only passes part of the response, it is wrong PLEASE ADD DOCUMENTATION TO ALL FUNCTIONS LIKE THIS! It would be a lot easier to contribute code if the main assumptions and goals of each function were documented --

That function was originally written by @ielis, but I can take a look at it and see if I can recreate and fix the bug after this has been pushed. I do think that this PR as it is is ready to be pushed though. @pnrobinson

@pnrobinson
Copy link
Collaborator Author

I am going to merge this, and now the code seems to be working again. I am not changing _vv.py now but we may need to do so, but let's make that a separate PR

@pnrobinson pnrobinson merged commit d163763 into develop Apr 23, 2024
5 checks passed
@pnrobinson pnrobinson deleted the draw-variants-transcript-and-protein branch April 23, 2024 16:06
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@lnrekerle lnrekerle lnrekerle approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
4 participants
@pnrobinson @lnrekerle @frehburg @ielis