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Quick fix in normalised scoring for cases where nrns/dps unnamed #48

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Quick fix in normalised scoring for cases where nrns/dps unnamed #48

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4 changes: 4 additions & 0 deletions R/scoremats.r
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,8 @@ sub_score_mat <- function(query, target, scoremat=NULL, distance=FALSE, normalis
if(!identical(length(dim(scoremat)),2L)) stop("scoremat must be a matrix!")

# Check for missing query and target neurons
if (is.null(rownames(scoremat)))
rownames(scoremat) <- as.character(1:nrow(scoremat))
rnames <- rownames(scoremat)
if(missing(target)) target <- rnames
else {
Expand All @@ -35,6 +37,8 @@ sub_score_mat <- function(query, target, scoremat=NULL, distance=FALSE, normalis
target <- intersect(target, rnames)
}
}
if (is.null(colnames(scoremat)))
colnames(scoremat) <- as.character(1:ncol(scoremat))
cnames=colnames(scoremat)
if(missing(query)) query <- cnames
else {
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4 changes: 4 additions & 0 deletions tests/testthat/test-NBLAST2.r
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Expand Up @@ -60,6 +60,10 @@ test_that("we can calculate normalised nblast v2 scores", {
expect_equal(nblast(testneurons[1], testneurons[3:5], version = 2, normalised = T),
baseline)

names(testneurons) <- NULL
scoresaba <- nblast_allbyall(testneurons, version=2,
normalisation = 'normalised')
expect_equal(dim(scoresaba), c(5, 5))
})

test_that("we can calculate scores for regular neurons",{
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