Update venice.R

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Signac
 Title: An analytics package for Single-cell data 
-Version: 0.0.10
+Version: 0.0.11
 Author: BioTuring INC.
 Maintainer: BioTuring <support@bioturing.com>
 Description: We introduce Signac, a versatile R package to facilitate the analysis workflow for single-cell data. It helps to find marker genes faster and more accurate, search for cells with similar expression profiles, integrate multiple datasets in the BioTuring Browser database (know more about BioTuring Browser), etc. For users with a limited computational resource, we provide the helper functions to exercise all analyses for the large-scale datasets from disk. Because of its speed and flexibility, it can be adapted to any existing R analysis pipeline to help explore single-cell data more efficient.
@@ -20,7 +20,7 @@ LinkingTo:
     RcppProgress,
     BH
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.2
 Suggests: 
     testthat
 Depends: 

R/venice.R

@@ -23,16 +23,16 @@ VeniceAllMarkers <- function(
   logfc.threshold = 0.25,
   nperm = 0
 ) {
-  data.use <-  Seurat:::GetAssayData(object = object[[assay]], slot = slot)
+  data.use <-  Seurat::GetAssayData(object = object[[assay]], slot = slot)
   MapVals <- function(vec, from, to) {
     vec2 <- setNames(object = to, nm = from)[as.character(x = vec)]
     vec2[is.na(x = vec2)] <- vec[is.na(x = vec2)]
     return(unname(obj = vec2))
   }
   if (is.null(x = node)) {
-    idents.all <- sort(x = unique(x = Seurat:::Idents(object = object)))
+    idents.all <- sort(x = unique(x = Seurat::Idents(object = object)))
   } else {
-    tree <- Seurat:::Tool(object = object, slot = 'BuildClusterTree')
+    tree <- Seurat::Tool(object = object, slot = 'BuildClusterTree')
     if (is.null(x = tree)) {
       stop("Please run 'BuildClusterTree' before finding markers on nodes")
     }
@@ -172,7 +172,7 @@ VeniceFindMarkers <- function(
 
   counts <- switch(
     EXPR = slot,
-    'scale.data' = Seurat:::GetAssayData(object = object[[assay]], slot = "counts"),
+    'scale.data' = Seurat::GetAssayData(object = object[[assay]], slot = "counts"),
     numeric()
   )
 
@@ -213,7 +213,7 @@ GetCellsIndices <- function(data.use, object, ident.1, ident.2) {
     tree <- if (is(object = ident.1, class2 = 'phylo')) {
       ident.1
     } else {
-      Seurat:::Tool(object = object, slot = 'BuildClusterTree')
+      Seurat::Tool(object = object, slot = 'BuildClusterTree')
     }
     if (is.null(x = tree)) {
       stop("Please run 'BuildClusterTree' or pass an object of class 'phylo' as 'ident.1'")
@@ -228,7 +228,7 @@ GetCellsIndices <- function(data.use, object, ident.1, ident.2) {
       stop(paste0("The following cell names provided to ident.1 are not present in the object: ", paste(bad.cells, collapse = ", ")))
     }
   } else {
-    ident.1 <- Seurat:::WhichCells(object = object, idents = ident.1)
+    ident.1 <- Seurat::WhichCells(object = object, idents = ident.1)
   }
   # if NULL for ident.2, use all other cells
   if (length(x = as.vector(x = ident.2)) > 1 &&
@@ -241,7 +241,7 @@ GetCellsIndices <- function(data.use, object, ident.1, ident.2) {
     if (is.null(x = ident.2)) {
       ident.2 <- setdiff(x = colnames(x = data.use), y = ident.1)
     } else {
-      ident.2 <- Seurat:::WhichCells(object = object, idents = ident.2)
+      ident.2 <- Seurat::WhichCells(object = object, idents = ident.2)
     }
   }
   ### Label the cells before finding marker genes: 1: Ident.1,  0: Ident2, >1:Other

src/RcppExports.cpp

@@ -7,6 +7,11 @@
 
 using namespace Rcpp;
 
+#ifdef RCPP_USE_GLOBAL_ROSTREAM
+Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
+Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
+#endif
+
 // FastGetCurrentDate
 Rcpp::Date FastGetCurrentDate();
 RcppExport SEXP _Signac_FastGetCurrentDate() {