Update tp53 module to add figures for manuscript

komalsrathi commented 3 years ago

Purpose/implementation Section

What scientific question is your analysis addressing?

Create and update plots for manuscript

What was your approach?

Create violin plots of TP53 scores across molecular subtype per broad histology. For these plots, I filtered molecular_subtype == NA | molecular_subtype == To be classified, sample count >= 3 and molecular subtype count > 1
Create violin plots of TP53 scores per cancer predisposition. For these plots, I removed cancer_predispositions == NA and tp53_score == NA.
Update ROC curves using a unified theme theme_pubr

What GitHub issue does your pull request address?

https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/1146

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

Plots of TP53 scores across molecular subtypes per broad histology

plots
├── TP53scores_Diffuse_astrocytic_and_oligodendroglial_tumor.png
├── TP53scores_Embryonal_tumor.png
├── TP53scores_Ependymal_tumor.png
├── TP53scores_Low-grade_astrocytic_tumor.png

P-value files for TP53 comparison with molecular subtypes per broad histology

results
├── TP53scores_Diffuse_astrocytic_and_oligodendroglial_tumor.tsv 
├── TP53scores_Embryonal_tumor.tsv
├── TP53scores_Ependymal_tumor.tsv
├── TP53scores_Low-grade_astrocytic_tumor.tsv

Output of 06-evaluate-classifier.py to be used for creating ROC curves in R

results
├── polya_TP53.tsv 
├── stranded_TP53.tsv

Updated ROC curves using 07-plot-roc.R

plots
├── polya_TP53_roc.png
├── stranded_TP53_roc.png

Plots of TP53 altered status for each of the cancer predispositions

plots
├── Li-Fraumeni\ syndrome_tp53_scores.png
├── NF-1,Other\ inherited\ conditions\ NOS_tp53_scores.png
├── NF-1_tp53_scores.png
├── NF-2,Schwannomatosis_tp53_scores.png
├── NF-2_tp53_scores.png
├── None\ documented_tp53_scores.png
├── Other\ inherited\ conditions\ NOS,Schwannomatosis_tp53_scores.png
├── Other\ inherited\ conditions\ NOS_tp53_scores.png
├── Schwannomatosis_tp53_scores.png
├── Tuberous\ Sclerosis_tp53_scores.png

Is there anything that you want to discuss further?

Should we remove:

1) Old version of Li-Fraumeni syndrome_tp53_scores.png

plots
├── lfs_tp53_scores.png

2) Old version of ROC plots that are now under plots/:

results
├── polya_TP53.png
├── stranded_TP53.png

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

Yes

Results

What types of results are included (e.g., table, figure)?

Tables, figures as specified above

What is your summary of the results?

N/A

Reproducibility Checklist

[x] The dependencies required to run the code in this pull request have been added to the project Dockerfile.
[x] This analysis has been added to continuous integration.

Documentation Checklist

[x] This analysis module has a README and it is up to date.
[x] This analysis is recorded in the table in analyses/README.md and the entry is up to date.
[x] The analytical code is documented and contains comments.

komalsrathi commented 3 years ago

@jharenza can you review this when you get a chance? I wasn't sure if you got notified about it.

jharenza commented 3 years ago

Yes, on my list for today!

komalsrathi commented 3 years ago

@jharenza I have made the following changes:
1) updated some output file names to be consistent and more meaningful 2) updated ROC with shuffled/non-shuffled data + using simpsons theme 3) updated README

komalsrathi commented 3 years ago

Ok, just fixed it. It was using wilcox by default but had 3 levels which weren't showing up. Now I am using a condition to use kruskal test for > 2 levels here

komalsrathi commented 3 years ago

I am not sure why the checks are failing, because it is running successfully on my local machine.

jharenza commented 3 years ago

sorry @jaclyn-taroni - missed tagging you in this for the CI failure

jaclyn-taroni commented 3 years ago

I am not sure why the checks are failing, because it is running successfully on my local machine.

To narrow things down – running locally using the Docker image and the CI data?

komalsrathi commented 3 years ago

I am not sure why the checks are failing, because it is running successfully on my local machine.

To narrow things down – running locally using the Docker image and the CI data?

No, I usually just run the bash script as is: cd OpenPBTA-analysis/analyses/tp53_nf1_score && bash run_classifier.sh

jaclyn-taroni commented 3 years ago

Based on the error:

Error: Column `shuffled` can't be modified because it's a grouping variable

I suspect the problem is this part of the code using the version of dplyr on the project image:

https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/1166/files#diff-493f7948a2d11d25184544297119530038ef44dfe0f2692706ea079a9cc04e19R12-R17

komalsrathi commented 3 years ago

@jaclyn-taroni ok I removed the unnecessary grouping I had in my code, all good now. Thanks!

AlexsLemonade / OpenPBTA-analysis