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Hotfix/fix gs get singlecell expression by gate #391

Merged
merged 4 commits into from
Aug 20, 2023
Merged

Hotfix/fix gs get singlecell expression by gate #391

merged 4 commits into from
Aug 20, 2023

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mikejiang
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@mikejiang mikejiang commented Aug 20, 2023 •
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fix cpp11 string conversion bug reported by #390

before

> library(flowWorkspace)
> dataDir <- system.file("extdata",package="flowWorkspaceData")
> gs_dir <- list.files(dataDir, pattern = "gs_manual",full = TRUE)
> gs <- load_gs(gs_dir)
> mat <- gs_get_singlecell_expression_by_gate(gs, "CD3+")
.Error: Expected string vector of length 1

after

> mat <- gs_get_singlecell_expression_by_gate(gs, "CD3+")
.
> head(mat)
$CytoTrol_CytoTrol_1.fcs
         CD3 V450     SSC-A
    [1,] 2996.536  91113.96
    [2,] 2749.284  76954.91
    [3,] 2507.708  70116.48
    [4,] 2657.550  66052.55

mikejiang
mikejiang commented Aug 20, 2023
View reviewed changes
tests/testthat/GatingSet-testSuite.R
@@ -467,16 +467,16 @@ test_that("add", {
gs_pop_remove("CD8_demo", gs = gs)
})

if(!isCpStaticGate)
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re-enable test

mikejiang
mikejiang commented Aug 20, 2023
View reviewed changes
src/getSingleCellExpression.cpp
@@ -70,17 +70,14 @@ cpp11::writable::doubles_matrix<> cpp_getSingleCellExpressionByGate(cpp11::exter
cpp11::strings pops(markers_pops.at(i));
// merge the indices from multiple nodes for the same marker
for(int j = 0; j < pops.size(); ++j){
string pop = cpp11::as_cpp<std::string>(pops[j]);
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this is offending line, where pops[j] doesn't appear to be cpp11:string anymore when pops is length of 1.
The fix is easy, remove explicit coercion, let cpp11 own magic auto coercion takes its place

@mikejiang mikejiang requested a review from gfinak August 20, 2023 03:55
@mikejiang mikejiang merged commit fefee28 into devel Aug 20, 2023
@mikejiang mikejiang mentioned this pull request Aug 20, 2023
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