diff --git a/DESCRIPTION b/DESCRIPTION index 04f2a9a..4ce04e3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: scmap Type: Package Title: A tool for unsupervised projection of single cell RNA-seq data -Version: 1.1.4 +Version: 1.1.5 Author: Vladimir Kiselev Maintainer: Vladimir Kiselev Authors@R: c(person("Vladimir", "Kiselev", diff --git a/R/CoreMethods.R b/R/CoreMethods.R index 53c0d27..aaf8000 100755 --- a/R/CoreMethods.R +++ b/R/CoreMethods.R @@ -475,4 +475,4 @@ scmapCell2Cluster.SingleCellExperiment <- function(scmapCell_results, cluster_li #' @rdname scmapCell2Cluster #' @aliases scmapCell2Cluster -setMethod("scmapCell2Cluster", "SingleCellExperiment", scmapCell2Cluster.SingleCellExperiment) +setMethod("scmapCell2Cluster", "list", scmapCell2Cluster.SingleCellExperiment) diff --git a/man/scmapCell2Cluster.Rd b/man/scmapCell2Cluster.Rd index d0f8e92..1090f80 100644 --- a/man/scmapCell2Cluster.Rd +++ b/man/scmapCell2Cluster.Rd @@ -5,22 +5,20 @@ \alias{scmapCell2Cluster} \alias{scmapCell2Cluster} \alias{scmapCell2Cluster.SingleCellExperiment} -\alias{scmapCell2Cluster,SingleCellExperiment-method} +\alias{scmapCell2Cluster,list-method} \alias{scmapCell2Cluster} \title{Approximate k-NN cell-type classification using scfinemap} \usage{ -scmapCell2Cluster(projection = NULL, scmapCell_results = NULL, - cluster_list = NULL, w = 3, threshold = 0.5) +scmapCell2Cluster(scmapCell_results = NULL, cluster_list = NULL, w = 3, + threshold = 0.5) -scmapCell2Cluster.SingleCellExperiment(projection, scmapCell_results, - cluster_list, w, threshold) +scmapCell2Cluster.SingleCellExperiment(scmapCell_results, cluster_list, w, + threshold) -\S4method{scmapCell2Cluster}{SingleCellExperiment}(projection = NULL, - scmapCell_results = NULL, cluster_list = NULL, w = 3, threshold = 0.5) +\S4method{scmapCell2Cluster}{list}(scmapCell_results = NULL, + cluster_list = NULL, w = 3, threshold = 0.5) } \arguments{ -\item{projection}{an object of \code{\link[SingleCellExperiment]{SingleCellExperiment}} class} - \item{scmapCell_results}{the output of `scmapCell()` with `projection` as its input.} \item{cluster_list}{list of cell cluster labels correspondint to each index against which the `projection` has been projected} @@ -53,6 +51,6 @@ sce <- sce[!duplicated(rownames(sce)), ] sce <- selectFeatures(sce) sce <- indexCell(sce) scmapCell_results <- scmapCell(sce, list(metadata(sce)$scmap_cell_index)) -sce <- scmapCell2Cluster(sce, scmapCell_results, cluster_list = list(colData(sce)$cell_type1)) +sce <- scmapCell2Cluster(scmapCell_results, cluster_list = list(colData(sce)$cell_type1)) } diff --git a/vignettes/scmap.Rmd b/vignettes/scmap.Rmd index 4373fe2..dc1a932 100755 --- a/vignettes/scmap.Rmd +++ b/vignettes/scmap.Rmd @@ -206,13 +206,13 @@ names(scmapCell_results) For each dataset there are two matricies. `cells` matrix contains the top 10 (`scmap` default) cell IDs of the cells of the reference dataset that a given cell of the projection dataset is closest to: ```{r} -scmapCell_results$xin$cells[,1:3] +scmapCell_results$yan$cells[,1:3] ``` `similarities` matrix contains corresponding cosine similarities: ```{r} -scmapCell_results$xin$similarities[,1:3] +scmapCell_results$yan$similarities[,1:3] ``` ## Cluster annotation @@ -221,7 +221,6 @@ If cell cluster annotation is available for the reference datasets, in addition ```{r} scmapCell_clusters <- scmapCell2Cluster( - sce, scmapCell_results, list( as.character(colData(sce)$cell_type1)