Fix lookups #173
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Fix lookups #173
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ogibson
reviewed
Sep 28, 2021
| # corresponding names stored in seurat object meta.data | ||
| seurat_keys <- scdata@misc$metadata_lookups[keys] | ||
| # same values used in construct_metadata | ||
| seurat_keys <- make.names(c('samples', keys), unique = TRUE)[-1] |
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I don't quite get why samples is here, because we already generate the samples cell_sets, right?
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it's just so that make.names has the same supplied values as it did in create_seurat
Codecov Report
@@ Coverage Diff @@
## master #173 +/- ##
==========================================
+ Coverage 54.72% 56.69% +1.96%
==========================================
Files 19 19
Lines 1239 1233 -6
==========================================
+ Hits 678 699 +21
+ Misses 561 534 -27
Continue to review full report at Codecov.
|
ogibson
approved these changes
Sep 29, 2021
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Background
The lookups were broken because
@miscslot get's overwritten by merging ofscdata_listLink to staging deployment URL
https://ui-olivergibson-p173.scp-staging.biomage.net/data-management
Links to any Pull Requests related to this
Anything else the reviewers should know about the changes here
Changes
Code changes
Definition of DONE
Your changes will be ready for merging after each of the steps below have been completed:
Testing
To set up easy local testing with inframock, follow the instructions here: https://github.com/biomage-ltd/inframock
To deploy to the staging environment, follow the instructions here: https://github.com/biomage-ltd/biomage-utils
Documentation updates
Is all relevant documentation updated to reflect the proposed changes in this PR?
Approvers
Just before merging:
unstagescript in here: https://github.com/biomage-ltd/biomage-utils is executed. This script cleans up your deployment to stagingOptional