Update for upcoming Matrix package update

cole-trapnell-lab · Oct 23, 2022 · b2e9cc3 · b2e9cc3
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: cicero
 Type: Package
 Title: Predict cis-co-accessibility from single-cell chromatin accessibility data
-Version: 1.13.4
+Version: 1.13.5
 Authors@R: c(
     person("Hannah", "Pliner", email = "hpliner@uw.edu", role = c("aut", "cre")), 
     person("Cole", "Trapnell", email = "coletrap@uw.edu", role = c("aut")))

diff --git a/R/activityScores.R b/R/activityScores.R
@@ -164,7 +164,10 @@ build_composite_gene_activity_matrix <- function(input_cds,
     total_linked_site_weights[is.finite(total_linked_site_weights) == FALSE] <- 0
     total_linked_site_weights[is.na(total_linked_site_weights)] <- 0
     total_linked_site_weights[is.nan(total_linked_site_weights)] <- 0
+    site_names <- names(total_linked_site_weights)
     total_linked_site_weights <- Matrix::Diagonal(x=total_linked_site_weights)
+    row.names(total_linked_site_weights) <- site_names
+    colnames(total_linked_site_weights) <- site_names
     scaled_site_weights <- total_linked_site_weights %*%
         promoter_conn_matrix[,distal_safe_sites, drop=FALSE] %*%
         scaled_site_weights