Fix SigScores ronames issue; Bump to 3.0.1

Author: deto

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: VISION
 Title: Functional interpretation of single cell RNA-seq latent manifolds
-Version: 3.0.0
+Version: 3.0.1
 Authors@R: c(person("Matt", "Jones", email = "mattjones315@gmail.com", role = c("aut", "cre")),
 			 person("David", "Detomaso", email = "david.detomaso@berkeley.edu", role = c("aut", "cre")),
 			 person("Tal", "Ashuach", email = "tal_ashuach@berkeley.edu", role = c("aut")),
@@ -43,7 +43,7 @@ Encoding: UTF-8
 LazyData: true
 URL: https://yoseflab.github.io/VISION, https://github.com/yoseflab/VISION
 BugReports: https://github.com/YosefLab/VISION/issues
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
 Suggests:
 	Biobase,
 	BiocStyle,

R/AnalysisFunctions.R

@@ -1118,7 +1118,7 @@ clusterSigScores <- function(object, variables = "All") {
 #' of a particular categorical trait with respect to a tree (as introduced
 #' with the metastatic score in Quinn, Jones et al Science 2021).
 #' 
-#' @importFrom phanghorn parsimony
+#' @importFrom phangorn parsimony
 #' @param object the PhyloVision object
 #' @return the object with new continuous covariates populated corresponding to the plasticities
 #' @export 

R/SigScoreMethods.R

@@ -97,6 +97,8 @@ innerEvalSignatureBatchNorm <- function(normData, sigs) {
     C <- (SRsE + SRsRo + SCo) %*% Cs
 
     sigScores <- as.matrix(C)
+    rownames(sigScores) <- rownames(sigSparseMatrix)
+    colnames(sigScores) <- colnames(normData@data)
 
     denom <- rowSums(abs(sigSparseMatrix)) # denom is vector of length N_sigs