Last ReadMe Updates and Figure Updates #9
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
elizabethmcd
approved these changes
Aug 20, 2024
| @@ -235,21 +226,21 @@ We used SnpSift (https://doi.org/10.3389/fgene.2012.00035), a component of the S | |||
| We ran: | |||
| `java -jar SnpSift.jar filter "(ANN[*].EFFECT has '\''missense_variant'\'' | ANN[*].EFFECT has '\''nonsense_variant'\'' | ANN[*].EFFECT has '\''frameshift_variant'\'')" data_generation/results/vcf/annotated_output.vcf.gz | bgzip > data_generation/results/vcf/output.non_silent.vcf.gz` | |||
|
|
|||
| #### Data analysis | |||
| ### 2- Data analysis | |||
There was a problem hiding this comment.
not sure I understand why there is the 2- in the header when I don't see a 1- before this?
| @@ -250,7 +250,8 @@ CDS_rate_comp=left_join(numb_cds,CDS_rate_sub, by='contigs') | |||
| CDS_rate_comp$ratio=CDS_rate_comp$numb_var_ns/CDS_rate_comp$numb_var_all | |||
|
|
|||
| dens_ratio=ggplot(CDS_rate_comp, aes(x=ratio))+ | |||
| geom_density(fill='#BABEE0')+theme_arcadia(x_axis_type = 'numerical') | |||
| geom_density(fill='#BABEE0')+theme_arcadia(x_axis_type = 'numerical')+ | |||
There was a problem hiding this comment.
can you make these new lines after the + so it is easier to read?
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
In this branch I have edited the ReadMe to address issues 2,3,6 and 7 and I have modified the code for the Figures in the R notebooks.
PR checklist
Tag the issue(s) or milestones this PR fixes (e.g.
Fixes #123, Resolves #456).I have addressed issues:
-# 2: 'how to rule the pipeline': here I have only added a couple of sentences to explain what type of code the project is associated with. There is no real possibility to explain per se how to 'run the pipeline' as the code shared in the repo represents all the different steps and tools used to generate the data. It encompasses multiple scripts and softwares that are not combined into a single pipeline
-# 3: I have added the DOI of the Zenodo repository in the ReadMe
-# 6: I have added a paragraph in the ReadMe (Data section) to explain how and what data we share
-# 7: I have added the information regarding Computer specifications in the appropriate section of the ReadMe
In the ReadMe:
In addition to addressing the issues in the ReadMe, I have made some formatting changes.
In R markdown and associated markdown notebooks:
I have edited the parts of the code that are associated with the Figures that are in the Pub to address Audrey's comments. The figures are now final and we shouldn't expect further changes.