Panel C Frequency Stacked Bar Plot

[runjin326]

Purpose/implementation Section

What scientific question is your analysis addressing?

Generate stacked bar plots for molecular subtypes with and without alterations.

What was your approach?

Use the histology file to match molecular subtypes and then plot out.

What GitHub issue does your pull request address?

https://github.com/d3b-center/Cole-telomere-analysis/issues/19

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

Which areas should receive a particularly close look?

Please check to see whether the subtypes are what we want to plot (they are different from the ones that you showed in the ticket). Currently, I output the chi-sq results to a txt file - please let me know whether that is fine.

Is there anything that you want to discuss further?

NA

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)?

Stacked barplot is in plots folder (mol_subtype_stacked.pdf) Chi-square result is in output folder (chi-sqaure-results.tsv)

What is your summary of the results?

Chi-square result: p-value = 0.02278

Reproducibility Checklist

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

Documentation Checklist

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

[jharenza]

Hmm, actually I think she only wanted us to compare H3 WT, H3 K28 and H3 G35, although this is also fascinating - can you add this as a second stacked barplot and chisq? Can you also output contingency tables?

[runjin326]

@jharenza - grouped together and output the table for chisq as well.