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This allows users to select row/column labels when creating an NG-CHM that will be visible in the NG-CHM viewer. Usage documentaiton and examples are in the panel_configuration constructor documentation.
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Pull Request Overview
This PR adds support for specifying panel selections by row/column labels and converts them to indices for the NG-CHM viewer.
- Introduces
selectionsparameter throughoutpanel_configurationclasses, methods, and documentation. - Implements label-to-index conversion via
convertPanelSelectionsFromLabelToIndex, plus file‐reading helpers. - Adds tests covering hclust, dendrogram, and label-based selection conversion.
Reviewed Changes
Copilot reviewed 9 out of 9 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
| tests/testthat/test-selections.R | New tests for converting label-based selections to indices |
| man/panel_configuration.Rd | Updated constructor docs to include selections and usage examples |
| man/panel_configuration-class.Rd | Added selections slot documentation |
| man/default_panel_configuration.Rd | Removed outdated default config docs |
| R/panelFunctions.R | Made default_panel_configuration internal and added default selections |
| R/panelClasses.R | Added selections slot and constructor argument to class |
| R/allMethods.R | Added convertPanelSelectionsFromLabelToIndex and hooked into chmMake |
| R/ngchmshaidy.R | Added getLabelsFromFile and getDendrogramOrderFromFile helpers |
| NAMESPACE | Removed export of default_panel_configuration |
Comments suppressed due to low confidence (1)
man/panel_configuration.Rd:45
- [nitpick] This sentence is duplicated; remove one occurrence to avoid redundancy in the documentation.
Each element must be a detailMap, summaryMap, or pluginPane object.
bmbroom
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Jul 16, 2025
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Adds an important capability to the NGCHM R package as discussed in weekly NG-CHM meeting.
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This pull request implements the "Selections from R" feature request.
This allows users to select row/column labels when creating an NG-CHM that will be visible in the NG-CHM viewer.
Usage documentation and examples are in the panel_configuration constructor documentation.
All tests pass, and
R CMD CHECK --as-cranyields no issues.