Replace sankey with alluvial plot

Nanostring-Biostats / GeoMxWorkflows

Workflows for analyzing data with the GeomxTools package and subsequent GeoMx related packages

MIT License

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Replace sankey with alluvial plot #27

Closed mahitha-raj closed 1 year ago

mahitha-raj commented 1 year ago

Fixes bug in ggplot2 by replacing the sankey diagram with an alluvial plot
Mirrors the fix uses in sDAS
Adds the 'parcats' and 'easyalluvial' packages to NAMESPACE

Note: I used target_demoData for the post-QC Aulluvial plot because the text mentioned removing both (i) segments flagged by QC, and (ii) low detection rate. In the original workflow, post-QC demoData was used.

mahitha-raj commented 1 year ago

All changes have been made and re-tested the knit. Ready for a follow-up review @NicoleEO .

maddygriz commented 1 year ago

@mahitha-raj @NicoleEO I fixed the DE plots. I added the changes here because I couldn't get the vignette to knit on the main branch due to the sankey issue. The alluvial plots look good!

NicoleEO commented 1 year ago

Resolves issue #21