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microbiome / iSEEtree

extension of iSEE for TreeSE
https://microbiome.github.io/iSEEtree/
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Add RowTreePlot to default panels for TreeSummarizedExperiment objects #1

Closed RiboRings closed 1 year ago

RiboRings commented 1 year ago

Given the following example, we see that RowTreePlot has to be specified in initial so that it is included in the panels to visualise.

library(mia)
data("GlobalPatterns", package = "mia")
tse <- GlobalPatterns

tse_genus <- mergeFeaturesByPrevalence(tse,
                                       rank = "Genus",
                                       prevalence = 50/100)

tse_genus <- addTaxonomyTree(tse_genus)
tse_genus <- transformAssay(tse_genus, method = "relabundance")

if (interactive()) {
  iSEE(tse_genus, initial=list(ColumnDataPlot(PanelId=1L),
                               RowTreePlot()))
}

Ideally, RowTreePlot should be made default panel for TreeSummarizedExperiment class so that it is returned automatically by this code:

if (interactive()) {
  iSEE(tse_genus)
}
RiboRings commented 1 year ago

It was fixed with commit https://github.com/RiboRings/iSEEtree/commit/a9209d71878024f830a0bfc20e8ad80afb5b2ce6