Fixing v14 breaking changes #523
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| @@ -20,20 +20,47 @@ jobs: | |||
| name: Sample Distribution Analyses | |||
| command: ./scripts/run_in_ci.sh bash "analyses/sample-distribution-analysis/run-sample-distribution.sh" | |||
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| # TODO: The data files for CI need to be fixed https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/527 | |||
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After the subset was redone, this doesn't rectify this?
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No it did not - more details in #527
| @@ -307,7 +304,7 @@ circos_map_plot( | |||
| ```{r} | |||
| circos_map_transloc(transloc_df, | |||
| add_track = FALSE, # We change this to true to add on to our already existing plot | |||
| sample_names = samples_for_examples[1], | |||
| sample_names = sample(transloc_df$biospecimen_id1, 1), | |||
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I had to do this because not all samples have BNDs so this will kick back an error.
| # Can't have identical y_min and y_max, this is just so CircleCI runs even if | ||
| # the subset data is wonky | ||
| if (y_min == y_max) { | ||
| y_max <- y_max + 0.001 |
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y_min and y_max are calculated based on the data, but with some of the subsets, you can get values that are identical and circlize doesn't like that. So this is my fix.
| allFuseEmbry <- allFuseEmbry %>% | ||
| prepareOutput(specimensUnion) | ||
| if (!running_in_ci) { | ||
| allFuseEmbry <- allFuseEmbry %>% |
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I don't really know what this means, but if it works 👍
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Before, we skipped the step for generating the fusions of interest file for EPN samples because they were not represented in the subset. Now I'm switching and running the EPN, skipping the non-ATRT, non-MB embryonal fusions and genes of interest because those are not represented but the EPN samples are.
Purpose/implementation Section
Here I am attempting to fix breaking changes that are coming up in CI as part of the v14 release.