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Fix conversion wide-to-long format #162

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Merged
ncborcherding merged 3 commits into from
Jun 5, 2025
Merged

Fix conversion wide-to-long format #162

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b796a44
ignore NAs for rowSums2(). This was throwing an error before when NAs…
toobiwankenobi Jun 5, 2025
273d1a1
fix the conversion from wide to long format. See issue #160
toobiwankenobi Jun 5, 2025
cad1c94
minor fix version bump
ncborcherding Jun 5, 2025
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: escape
Title: Easy single cell analysis platform for enrichment
Version: 2.5.3
Version: 2.5.4
Authors@R: c(
person(given = "Nick", family = "Borcherding", role = c("aut", "cre"), email = "ncborch@gmail.com"),
person(given = "Jared", family = "Andrews", role = c("aut"), email = "jared.andrews07@gmail.com"),
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6 changes: 6 additions & 0 deletions NEWS.md
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@@ -1,3 +1,9 @@
# 2.5.4 (2025-06-05)

## Bug fixes
* Fix conversion wide-to-long format for ```heatmapEnrichment()```
* Fix issue with t() call on sparse matrices.

# 2.5.3 (2025-05-19)

## Highlights
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2 changes: 1 addition & 1 deletion R/heatmapEnrichment.R
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Expand Up @@ -96,7 +96,7 @@ heatmapEnrichment <- function(input.data,
# ---------- 4. long format for ggplot (base-R) --------------------------
long <- data.frame(
variable = rep(gene.set, each = nrow(agg)),
value = as.vector(t(agg[gene.set])),
value = unlist(agg[gene.set], use.names = FALSE),
group = rep(agg[[group.by]], times = length(gene.set)),
stringsAsFactors = FALSE
)
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2 changes: 1 addition & 1 deletion R/utils.R
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Expand Up @@ -185,7 +185,7 @@
}
loadNamespace("DelayedMatrixStats")
}
cnts[MatrixGenerics::rowSums2(cnts) != 0, , drop = FALSE]
cnts[MatrixGenerics::rowSums2(cnts, na.rm = TRUE) != 0, , drop = FALSE]
}

# -----------------------------------------------------------------------------
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