lianos / sparrow.shiny Goto Github PK
View Code? Open in Web Editor NEWProvides shiny components to visualize sparrow GSEA results
Home Page: https://lianos.github.io/sparrow.shiny/
License: Other
Provides shiny components to visualize sparrow GSEA results
Home Page: https://lianos.github.io/sparrow.shiny/
License: Other
Reproducible example which ungracefully errors:
> db_single <- sparrow::GeneSetDb(
+ tibble::tribble(
+ ~collection, ~name, ~feature_id, ~symbol,
+ "some_coll", "some_name", "some_id", "some_symbol"
+ )
+ )
>
> sparrow.shiny::SparrowResultContainer(db_single)
Warning in .local(x, ...) :
Deactivating 1 gene sets because conformation of GeneSetDb to the target creates gene sets smaller than 2 or greater than Inf
Error in featureIds(geneSetDb(x), i, j, value = value, active.only = TRUE, :
collection (i) must be length 1 character vectors
With at least one set with multiple features, the call completes:
> db_multiple <- sparrow::GeneSetDb(
+ tibble::tribble(
+ ~collection, ~name, ~feature_id, ~symbol,
+ "some_coll", "_name", "some_id", "some_symbol",
+ "other_coll", "other_name", "other_id1", "other_symbol1",
+ "other_coll", "other_name", "other_id2", "other_symbol2"
+ )
+ )
>
> sparrow.shiny::SparrowResultContainer(db_multiple)
Warning in .local(x, ...) :
Deactivating 1 gene sets because conformation of GeneSetDb to the target creates gene sets smaller than 2 or greater than Inf
$mg
SparrowResult (max FDR by collection set to 0.20%)
---------------------------------------------------
No GSEA methods were run, only geneset level statistics calculated
$methods
character(0)
$choices
collection label value
1: other_coll other_name other_coll_::_other_name
attr(,"class")
[1] "SparrowResultContainer" "list"
If the SparrowResultContainer
requires 2+ feature sets, then I would expect the first call to return an empty result successfully.
The DT::datatable
that is generated by the renderFeatureStatsDataTable
module does some rewriting of the text in the name/symbol column to link out to a reference page.
When we sort the table by the symbol column, it sorts by the html in that column, rather than the symbol itself. This causes the rows to ultimately be sorted by the feature_id
of the feature because the feature_id
is ultimately used in the <a href=".."></a>
link that gets embedded in that colum
We have it running for sparrow, but never set this up. Let's do that.
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