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Hotfix/fix gs get singlecell expression by gate #391

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Aug 20, 2023
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2 changes: 1 addition & 1 deletion DESCRIPTION
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Package: flowWorkspace
Type: Package
Title: Infrastructure for representing and interacting with gated and ungated cytometry data sets.
Version: 4.13.1
Version: 4.13.2
Date: 2011-06-10
Author: Greg Finak, Mike Jiang
Maintainer: Greg Finak <[email protected]>, Mike Jiang <[email protected]>
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5 changes: 1 addition & 4 deletions src/getSingleCellExpression.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -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

VertexID u = gh.getNodeID(pop);
VertexID u = gh.getNodeID(pops[j]);
BoolVec ind = gh.getNodeProperty(u).getIndices();
if(j == 0)
indexList.at(i) = ind;
else{
transform(ind.begin(), ind.end(), indexList.at(i).begin(), indexList.at(i).begin(), logical_or<bool>());
}

}

}

cpp11::writable::doubles_matrix<> output = maskMatrix(indexList, data, threshold);
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39 changes: 20 additions & 19 deletions tests/testthat/GatingSet-testSuite.R
Original file line number Diff line number Diff line change
Expand Up @@ -467,16 +467,16 @@ test_that("add", {
gs_pop_remove("CD8_demo", gs = gs)
})

if(!isCpStaticGate)
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re-enable test

{


test_that("gs_get_singlecell_expression for COMPASS",{
nodes <- c('CD8/38- DR+', 'CD8/CCR7- 45RA+')

thisRes <- gs_get_singlecell_expression(gs, nodes, map = list("CD8/38- DR+" = "CD38 APC", "CD8/CCR7- 45RA+" = "CCR7 PE"))
expectRes <- readRDS(file.path(resultDir, "getData_COMPASS_gs.rds"))
# browser()

expect_equal(thisRes,rev(expectRes),tol = 1e-07)




#test other.markers (redundant marker should be merged automatically)
thisRes <- gs_get_singlecell_expression(gs, nodes
Expand All @@ -503,32 +503,33 @@ if(!isCpStaticGate)
), "number of markers")
#marginal = FALSE
thisRes <- gs_get_singlecell_expression(gs, nodes, marginal = FALSE)
expect_equal(thisRes[[1]][,c("CD38 APC", "CCR7 PE")],expectRes[[1]],tol = 1e-07)
expect_equal(thisRes[[1]][,1] == 0, thisRes[[1]][,2] == 0)



#gates share the same marker
nodes <- c('CD8/38- DR+', "CD8/38+ DR-", 'CD8/CCR7- 45RA+')
thisRes <- gs_get_singlecell_expression(gs, nodes, marginal = FALSE)
#TODO: gh_pop_get_indices_mat api is somehow broken, since rarely used, not going to fix until asked for
#verify the results by calling R routines
nodes.expr <- quote(`CD8/38- DR+|CD8/38+ DR-|CD8/CCR7- 45RA+`)
ind.total <- getIndices(gs[1], nodes.expr)[[1]]
ind.mat <- gh_pop_get_indices_mat(gs[[1]], nodes.expr)
#Or the ind for the same marker from nodes
ind.DR <- ind.38 <- ind.mat[,1] | ind.mat[,2]
ind.CCR <- ind.45 <- ind.mat[,3]
#masking
mat <- exprs(gh_pop_get_data(gs[[1]]))[,c(6, 9, 10, 11)]
mat <- mat * c(ind.38, ind.DR, ind.CCR, ind.45)
mat <- mat[ind.total, ]
expect_equal(thisRes[[1]], mat, check.attributes = FALSE)
# nodes.expr <- quote(`CD8/38- DR+|CD8/38+ DR-|CD8/CCR7- 45RA+`)
# ind.total <- ncdfFlow::getIndices(gs[1], nodes.expr)[[1]]
# ind.mat <- gh_pop_get_indices_mat(gs[[1]], nodes.expr)
# #Or the ind for the same marker from nodes
# ind.DR <- ind.38 <- ind.mat[,1] | ind.mat[,2]
# ind.CCR <- ind.45 <- ind.mat[,3]
# #masking
# mat <- exprs(gh_pop_get_data(gs[[1]]))[,c(6, 9, 10, 11)]
# mat <- mat * c(ind.38, ind.DR, ind.CCR, ind.45)
# mat <- mat[ind.total, ]
# expect_equal(thisRes[[1]], mat, check.attributes = FALSE)

#gs_get_singlecell_expression_by_gate associated with channel that does not have markers
mat <- gs_get_singlecell_expression_by_gate(gs, "CD3+")
expect_equal(colnames(mat[[1]]), c("CD3 V450", "SSC-A"))
expect_equal(nrow(mat[[1]]), gh_pop_get_count(gs[[1]], "CD3+"))
})

}



test_that("markernames", {
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