modified subset tree

Author: Yanay1

R/methods-Vision.R

@@ -119,7 +119,10 @@ setMethod("Vision", signature(data = "matrixORSparse"),
             }
 
             if (!is.null(tree)) {
-                data = data[,tree$tip.label]
+                # Subset matrix
+                data <- data[,tree$tip.label]
+                # Subset Tree
+                tree <- keep.tip(tree, colnames(data)) 
             }
 
             .Object@exprData <- data

docs/articles/phyloVision.html

@@ -11,7 +11,7 @@ articles:
   web_only/10xData: 10xData.html
   web_only/Seurat: Seurat.html
   web_only/SignatureAutocorrelation: SignatureAutocorrelation.html
-last_built: 2021-08-19T18:21Z
+last_built: 2021-08-19T18:40Z
 urls:
   reference: https://yoseflab.github.io/VISION//reference
   article: https://yoseflab.github.io/VISION//articles

docs/articles/trajectories.html

@@ -68,7 +68,7 @@ vis <- PhyloVision(tree=tree, data=expr, signatures=sig, meta=meta, num_neighbor
 ```
 **Tree**
 
-The `ape` phylogeny object. Singleton edges should be collapsed prior to use. The tree should be filtered to have the same cell (leaf) names as the expression data.
+The `ape` phylogeny object. Singleton edges should be collapsed prior to use. Ensure that leaf names correspond to same names used in the expression matrix. 
 
 **Expression Data**
 

docs/pkgdown.yml

@@ -23,6 +23,8 @@ set.seed(6473) ## for reproducibility
 
 # Introduction
 
+*Note: this feature is deprecated in VISION 3.0+.*
+
 To compute Signature consistency scores, VISION needs a cell-cell similarity metric in order to
 build the neighborhood graph.  By default, VISION runs PCA and uses euclidean distances in the reduced
 space for this purpose.  However, if the cells' variation is better modeled by a trajectory (either