Add plot exports, ported amRml visualizations, and network styling#32
Add plot exports, ported amRml visualizations, and network styling#32eboyer221 wants to merge 1 commit into
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This PR is big and utils in particualr has become quite challenging to read. We have decided to first reorganize the code in a separate PR and rebase. In addition after this reorganization, thevarious features here may be split into smaller PRs.
Leaving this PR open for now
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Rebased onto The only real conflict was
After a fresh Still on the to-do list for this PR (per our chat): the export-observer race |
Summary
This PR adds the cross-drug generalization heatmap, adds several plots from amRml, gives every dashboard panel a dedicated export button, and restyles the interaction networks to have shapes rather than only colors for the legend.
It also resolves the outstanding
BiocCheckwarning "No Bioconductor dependencies detected" since amRviz now depends on ComplexHeatmap (used for the static heatmap exports).Exports
Ported from amRml (PR #8)
Networks
Styling
Dependencies
Imports: ComplexHeatmap, circlize, RColorBrewer, grid, grDevices, htmlwidgets.Suggests: webshot2 (chromote already present).biocViewsupdated to valid software terms; READMEs synced.Testing
Testing
Added 5 test files covering the new functionality:
test-crossDrugHeatmap.R- cross-drug matrix prep, ComplexHeatmap object, plotly panel, PDF rendertest-portedPlots.R-makeTopFeatsVIPlot,makeMDRPerformancePlot,loadMDRResultstest-heatmapExport.R-makeHeatmapExport/.plotlyHeatmapMatrix/.writeHeatmapPdftest-widgetExport.R-.writeWidgetStatic(incl. a real headless-Chrome snapshot) +.exportBtntest-network.R- added assertions for the node-shape/legend hook and shared font