diff --git a/DESCRIPTION b/DESCRIPTION index c9c28c1..416e9d8 100644 --- a/DESCRIPTION +++ b/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 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: diff --git a/R/venice.R b/R/venice.R index bee24ff..5867d74 100644 --- a/R/venice.R +++ b/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 diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp index d0ec283..920f4d6 100644 --- a/src/RcppExports.cpp +++ b/src/RcppExports.cpp @@ -7,6 +7,11 @@ using namespace Rcpp; +#ifdef RCPP_USE_GLOBAL_ROSTREAM +Rcpp::Rostream& Rcpp::Rcout = Rcpp::Rcpp_cout_get(); +Rcpp::Rostream& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get(); +#endif + // FastGetCurrentDate Rcpp::Date FastGetCurrentDate(); RcppExport SEXP _Signac_FastGetCurrentDate() {