v2.1.0 commit

Author: deto

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: VISION
 Title: Functional interpretation of single cell RNA-seq latent manifolds
-Version: 2.0.0
+Version: 2.1.0
 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")),

NEWS.md

@@ -1,3 +1,17 @@
+# VISION 2.1.0
+
+Added parameter `sig_gene_threshold` with **changed default behavior**
+
+* Before it was a guideline to filter lowly expressed genes before running VISION
+* Now, by default, genes expressed in fewer than 0.1% of cells will be filtered automatically
+
+Bug Fixes:
+
+* Better colors in output when more than 10 categories
+* Errors with certain output object accessors
+* Selections not saving when loading results server
+* Crashes when running on more than 1200 signatures
+
 # VISION 2.0.0
 
 Lots of changes for this version.

R/methods-Vision.R

@@ -79,7 +79,7 @@ setMethod("Vision", signature(data = "matrixORSparse"),
                     unnormalizedData = NULL, meta=NULL,
                     projection_genes=c("fano"),
                     min_signature_genes=5,
-                    sig_gene_threshold=.005,
+                    sig_gene_threshold=.001,
                     threshold=.05, perm_wPCA=FALSE,
                     projection_methods = c("tSNE30"),
                     sig_norm_method = c("znorm_columns", "none", "znorm_rows",