🖼 Change `tpm/gene-disease-gtex` boxplot title

[logstar]

Pull Request Template

Description

Changed tpm/gene-disease-gtex/plot boxplot title from "Primary tumor vs GTEx tissue bulk gene expression" to "Primary tumor and GTEx tissue bulk gene expression", as suggested by @taylordm .

Changed "vs" to "and" to clarify that the boxplot does not imply any differential expression.

Resolves #40 .

Type of change

Non-breaking change.

Changed

• Changed tpm/gene-disease-gtex/plot boxplot title from "Primary tumor vs GTEx tissue bulk gene expression" to "Primary tumor and GTEx tissue bulk gene expression".

How Has This Been Tested?

• [x] Integration test

**Terminal returns for testing DEV host. Click to expand.**

```text $ git st On branch logstar/boxplot-title Your branch is up to date with 'origin/logstar/boxplot-title'. nothing to commit, working tree clean $ rm tests/http_response_output_files/png/*.png tests/http_response_output_files/json/*.json tests/results/*.tsv $ API_HOST=dev ./tests/curl_test_endpoints.sh ... GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/json?ensemblId=ENSG00000213420&efoId=EFO_0000621 http_code: 200 content_type: application/json time_total: 0.713590 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000213420&efoId=EFO_0000621&yAxisScale=linear http_code: 200 content_type: image/png time_total: 2.254655 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000213420&efoId=EFO_0000621&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 2.222131 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/json?ensemblId=ENSG00000213420&efoId=Orphanet_178 http_code: 200 content_type: application/json time_total: 0.651065 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000213420&efoId=Orphanet_178&yAxisScale=linear http_code: 200 content_type: image/png time_total: 1.989635 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000213420&efoId=Orphanet_178&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 2.221113 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/json?ensemblId=ENSG00000213420&efoId=MONDO_0016718 http_code: 200 content_type: application/json time_total: 0.649093 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000213420&efoId=MONDO_0016718&yAxisScale=linear http_code: 200 content_type: image/png time_total: 2.249565 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000213420&efoId=MONDO_0016718&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 2.162209 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/json?ensemblId=ENSG00000213420&efoId=MONDO_0016680 http_code: 200 content_type: application/json time_total: 0.630144 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000213420&efoId=MONDO_0016680&yAxisScale=linear http_code: 200 content_type: image/png time_total: 2.214019 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000213420&efoId=MONDO_0016680&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 2.187007 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/json?ensemblId=ENSG00000213420&efoId=MONDO_0016685 http_code: 200 content_type: application/json time_total: 0.705911 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000213420&efoId=MONDO_0016685&yAxisScale=linear http_code: 200 content_type: image/png time_total: 2.365181 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000213420&efoId=MONDO_0016685&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 2.132927 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-all-cancer/json?ensemblId=ENSG00000213420 http_code: 200 content_type: application/json time_total: 0.596141 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-all-cancer/plot?ensemblId=ENSG00000213420&yAxisScale=linear http_code: 200 content_type: image/png time_total: 1.583007 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-all-cancer/plot?ensemblId=ENSG00000213420&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 1.615866 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/json?ensemblId=ENSG00000157764&efoId=EFO_0000621 http_code: 200 content_type: application/json time_total: 0.646784 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000157764&efoId=EFO_0000621&yAxisScale=linear http_code: 200 content_type: image/png time_total: 2.164203 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000157764&efoId=EFO_0000621&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 2.425747 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/json?ensemblId=ENSG00000157764&efoId=Orphanet_178 http_code: 200 content_type: application/json time_total: 0.632829 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000157764&efoId=Orphanet_178&yAxisScale=linear http_code: 200 content_type: image/png time_total: 2.201664 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000157764&efoId=Orphanet_178&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 2.142722 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/json?ensemblId=ENSG00000157764&efoId=MONDO_0016718 http_code: 200 content_type: application/json time_total: 0.638697 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000157764&efoId=MONDO_0016718&yAxisScale=linear http_code: 200 content_type: image/png time_total: 2.160919 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000157764&efoId=MONDO_0016718&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 2.185793 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/json?ensemblId=ENSG00000157764&efoId=MONDO_0016680 http_code: 200 content_type: application/json time_total: 0.641936 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000157764&efoId=MONDO_0016680&yAxisScale=linear http_code: 200 content_type: image/png time_total: 2.165889 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000157764&efoId=MONDO_0016680&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 2.135561 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/json?ensemblId=ENSG00000157764&efoId=MONDO_0016685 http_code: 200 content_type: application/json time_total: 0.634513 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000157764&efoId=MONDO_0016685&yAxisScale=linear http_code: 200 content_type: image/png time_total: 2.178168 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000157764&efoId=MONDO_0016685&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 2.197299 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-all-cancer/json?ensemblId=ENSG00000157764 http_code: 200 content_type: application/json time_total: 0.615373 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-all-cancer/plot?ensemblId=ENSG00000157764&yAxisScale=linear http_code: 200 content_type: image/png time_total: 1.593838 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-all-cancer/plot?ensemblId=ENSG00000157764&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 1.580416 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/json?ensemblId=ENSG00000273032&efoId=EFO_0000621 http_code: 200 content_type: application/json time_total: 0.810669 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000273032&efoId=EFO_0000621&yAxisScale=linear http_code: 200 content_type: image/png time_total: 2.622353 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000273032&efoId=EFO_0000621&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 2.383565 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/json?ensemblId=ENSG00000273032&efoId=Orphanet_178 http_code: 200 content_type: application/json time_total: 0.966226 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000273032&efoId=Orphanet_178&yAxisScale=linear http_code: 200 content_type: image/png time_total: 2.159933 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000273032&efoId=Orphanet_178&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 2.193736 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/json?ensemblId=ENSG00000273032&efoId=MONDO_0016718 http_code: 200 content_type: application/json time_total: 0.790287 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000273032&efoId=MONDO_0016718&yAxisScale=linear http_code: 200 content_type: image/png time_total: 2.148597 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000273032&efoId=MONDO_0016718&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 2.365724 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/json?ensemblId=ENSG00000273032&efoId=MONDO_0016680 http_code: 200 content_type: application/json time_total: 0.782608 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000273032&efoId=MONDO_0016680&yAxisScale=linear http_code: 200 content_type: image/png time_total: 2.438213 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000273032&efoId=MONDO_0016680&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 2.547309 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/json?ensemblId=ENSG00000273032&efoId=MONDO_0016685 http_code: 200 content_type: application/json time_total: 0.794328 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000273032&efoId=MONDO_0016685&yAxisScale=linear http_code: 200 content_type: image/png time_total: 2.444436 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000273032&efoId=MONDO_0016685&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 2.386278 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-all-cancer/json?ensemblId=ENSG00000273032 http_code: 200 content_type: application/json time_total: 1.061237 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-all-cancer/plot?ensemblId=ENSG00000273032&yAxisScale=linear http_code: 200 content_type: image/png time_total: 1.776926 seconds GET https://openpedcan-api-dev.d3b.io/tpm/gene-all-cancer/plot?ensemblId=ENSG00000273032&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 1.721444 seconds $ git st On branch logstar/boxplot-title Your branch is up to date with 'origin/logstar/boxplot-title'. nothing to commit, working tree clean ```

Checklist

• [x] My code follows the style guidelines of this project
• [x] I have performed a self-review of my own code
• [x] I have commented my code, particularly in hard-to-understand areas
• [NA] I have made corresponding changes to the documentation
• [x] My changes generate no new warnings
• [NA] I have added tests that prove my fix is effective or that my feature works
• [NA] New and existing unit tests pass locally with my changes
• [NA] Any dependent changes have been merged and published in downstream modules
• [x] I have checked my code and corrected any misspellings
• [x] I have emojis in my PR and commits 😉

[afarrel]

Hi @logstar. Thank you for working on this module. Do the plots only use data from primary tumors or do they also contain data from relapsed tumors? If they contain data from relapsed/recurrent tumors then "Primary Tumor" may be misleading and should be renamed to simply Tumor and GTEx tissue gene expression.

[logstar]

Hi @logstar. Thank you for working on this module. Do the plots only use data from primary tumors or do they also contain data from relapsed tumors? If they contain data from relapsed/recurrent tumors then "Primary Tumor" may be misleading and should be renamed to simply Tumor and GTEx tissue gene expression.

Thank you for the question. Only primary tumors are used to generate the plots.

https://github.com/PediatricOpenTargets/OpenPedCan-api/blob/f6c10f6df13d34ba4764d6bde29ceb1e30bd9806/db/build_tools/tpm_data_lists.R#L54-L69

[logstar]

Looks good @logstar . Thanks for getting the changes in and answering my question.

@afarrel - Thank you for reviewing. I will merge this PR soon.