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

Update Fork #1

Open
wants to merge 247 commits into
base: master
Choose a base branch
from
Open

Update Fork #1

wants to merge 247 commits into from

Conversation

xtmgah
Copy link
Owner

@xtmgah xtmgah commented Aug 20, 2020

No description provided.

ebergstr and others added 30 commits September 21, 2018 12:39
@ebergstr
Delete SBS_mutation_count_plotting.R
8eeb2fa
@ebergstr
Delete README.pdf
153887a
@ebergstr
Delete rain_plots_BRCA.R
431214f
Updated as a Python package
df72b37
Added support for percentage input
ee4dfcc
Fixed y-axis issue when plotting percentages.
ac6bc61
Added percentage option
cb63a17
Check update. No new features.
5506ada
Added and example script and adapted the README file.
6c1c46a
Fixed 192 y-axis plots when mutation counts never exceed 4 mutations
ac1742d
Allow a space in signature/sample names
18b0b47
Fixed ordering issue of mutation types for users with older versions …
65af064 
…of python
Adjust function names, added plot_type argument, removed signature bo…
4c2bdea 
…olean argumnet, updated README
Added output folder
14a02dc
Fixed typos in README
1b20d4c
Fixed scaling issues. Added new parameter [plot_type]
840d86c
Added functions for plotting 6, 24, TSB DINUC, TSB INDELs
3ab895b
Update aligned with pypi package version 0.1.16 (1_Feb_2019). Fixed F…
163743b 
…ont cache issue with matplotlib.
Introduced support for PCAWG format.
30e0e34
Fixed issue with microhomologies in INDEL 83 plot
3ea6785
Added sample portrait script
b0157f7
Fixed normalized y-axis for sparse samples
30cc70c
Adjusted 1536 plot
389abb4
Fixed 1536 percentage bug
eb8e0a8
Fixed issue with ID-83 producing corrupted files
73d037f
Changed ID-TSB plot
a0a66af
Fixed ID-83 error
3e0486c
Fixed DINUC TSB plot, INDEL TSB plot, added versioning function
b38e397
Added matrix validation warning/exit
7ea1eb6
Update to sample portrait
e8f6b84
mdbarnesUCSD and others added 30 commits September 15, 2023 14:18
@mdbarnesUCSD
Merge pull request #40 from AlexandrovLab/u58
4b67712 
Upgrade to v1.3.16
@rvangara
lines 149 and 150, logic for checking input index column is updated
48ec00d
@mdbarnesUCSD
Upgrade v1.3.17: Update input handling to use deepcopy
6b1d26c
@mdbarnesUCSD
Merge pull request #41 from AlexandrovLab/corrections_ravi
1f6fd29 
lines 149 and 150, logic for checking input index column is updated
@mdbarnesUCSD
Upgrade v1.3.18: Update SV and CNV output handling to support pdf, pn…
13ed319 
…g, pil_image.
@mdbarnesUCSD
Add tests from @MousumyCSE
a9af24b
@mdbarnesUCSD
Update CNV/SV calls with new parameters in plot_example.py
06c332f
@mdbarnesUCSD
Update README
85f7535
@mdbarnesUCSD
Merge pull request #42 from AlexandrovLab/merge-u59
faafb4c 
Merge u59
@mdbarnesUCSD
Apply formatting changes
a29aa6f
@mdbarnesUCSD
Remove old input processing code
fd5d747
@mdbarnesUCSD
V1.3.19 Updates:
66f2594 
1. Refactor and test for handling Dataframes as input (add threshold 1e-4)
2. Fix for plotSV input handling (closes #43)
@mdbarnesUCSD
Merge pull request #44 from AlexandrovLab/u59b
99a1418 
U59b
@mdbarnesUCSD
Upgrade v1.3.20: Add np.ndarray to process_input
a57d54d
@mdbarnesUCSD
Merge pull request #45 from AlexandrovLab/u_ndarray
1feb78a 
Upgrade v1.3.20: Add np.ndarray to process_input
@mdbarnesUCSD
Add CLI and container updates
76c1408
@mdbarnesUCSD
Merge pull request #46 from AlexandrovLab/docker_cli
41c7247 
Add CLI and container updates
@mdbarnesUCSD
Update test threshold for difference
d7818ec
@mdbarnesUCSD
Update input handling to accomodate irregular index.name values
e5977db
@mdbarnesUCSD
Upgrade v1.3.22: Update input_processing index.name handling to be mo…
e5b1360 
…re robust.
@mdbarnesUCSD
Merge pull request #47 from AlexandrovLab/u_input_handling
941e5d4 
U input handling
@mdbarnesUCSD
Upgrade v1.3.23: Update SBS4608 custom_text_upper, custom_text_lower,…
3b8618e 
… custom_text_middle.
@mdbarnesUCSD
Merge pull request #48 from AlexandrovLab/4608_text
dbe0f27 
Upgrade v1.3.23: Update SBS4608 custom_text_upper, custom_text_lower,…
@mdbarnesUCSD
Fix: Ensure correct file path construction with os.path.join()
65f7f0e
@mdbarnesUCSD
Add environmental variable SIGPROFILERPLOTTING_VOLUME
630e241
@mdbarnesUCSD
Improve CLI boolean handling
ab30fbd
@mdbarnesUCSD
Stop creating output directory when PIL_Image is the savefig_format
59b6d63
@mdbarnesUCSD
Upgrade v1.3.24
4881b64 
1. Resolve issues with CLI boolean handling
2. Add support for environmental variable SIGPROFILERPLOTTING_VOLUME
3. Improve file path construction
4. Stop creation of output directory for savefig_format PIL_Image
5. Add Changelog
@mdbarnesUCSD
Improve plotting plot_type error messages
1e541a4
@mdbarnesUCSD
Merge pull request #50 from AlexandrovLab/development
db6d54c 
Development
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
6 participants
@xtmgah @ebergstr @azhark2 @mdbarnesUCSD @rvangara @Tina04021997