diff --git a/DESCRIPTION b/DESCRIPTION index d7293d60..4c23dfb6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: clustifyr Title: Classifier for Single-cell RNA-seq Using Cell Clusters -Version: 1.17.1 +Version: 1.17.2 Description: Package designed to aid in classifying cells from single-cell RNA sequencing data using external reference data (e.g., bulk RNA-seq, scRNA-seq, microarray, gene lists). A variety of correlation based methods and gene list enrichment methods are provided to assist cell @@ -8,11 +8,11 @@ Description: Package designed to aid in classifying cells from single-cell RNA s Authors@R: c(person(given = "Rui", family = "Fu", - role = "aut", - email = "raysinensis@gmail.com"), + role = c("cre", "aut"), + email = "ray.sinensis@gmail.com"), person(given = "Kent", family = "Riemondy", - role = c("cre", "aut"), + role = "aut", email = "kent.riemondy@gmail.com"), person(given = "Austin", family = "Gillen", diff --git a/man/assess_rank_bias.Rd b/man/assess_rank_bias.Rd index 5c2dac8b..28b46910 100644 --- a/man/assess_rank_bias.Rd +++ b/man/assess_rank_bias.Rd @@ -41,7 +41,7 @@ Find rank bias \examples{ \dontrun{ avg <- average_clusters( - pbmc_matrix_small, + pbmc_matrix_small, pbmc_meta$seurat_clusters ) res <- clustify( @@ -59,8 +59,8 @@ top_call <- cor_to_call( threshold = 0.8 ) res_rank <- assess_rank_bias( - avg, - cbmc_ref, + avg, + cbmc_ref, res = top_call ) } diff --git a/man/build_atlas.Rd b/man/build_atlas.Rd index f0981519..d0a7e6b7 100644 --- a/man/build_atlas.Rd +++ b/man/build_atlas.Rd @@ -29,10 +29,10 @@ Function to combine records into single atlas } \examples{ pbmc_ref_matrix <- average_clusters( -mat = pbmc_matrix_small, -metadata = pbmc_meta, -cluster_col = "classified", -if_log = TRUE # whether the expression matrix is already log transformed + mat = pbmc_matrix_small, + metadata = pbmc_meta, + cluster_col = "classified", + if_log = TRUE # whether the expression matrix is already log transformed ) references_to_combine <- list(pbmc_ref_matrix, cbmc_ref) atlas <- build_atlas(NULL, human_genes_10x, references_to_combine, NULL) diff --git a/man/calc_distance.Rd b/man/calc_distance.Rd index 697c51ad..753e4d8d 100644 --- a/man/calc_distance.Rd +++ b/man/calc_distance.Rd @@ -31,12 +31,14 @@ Distance calculations for spatial coord \examples{ cbs <- paste0("cb_", 1:100) -spatial_coords <- data.frame(row.names = cbs, - X = runif(100), - Y = runif(100)) +spatial_coords <- data.frame( + row.names = cbs, + X = runif(100), + Y = runif(100) +) group_ids <- sample(c("A", "B"), 100, replace = TRUE) dist_res <- calc_distance( - spatial_coords, + spatial_coords, group_ids ) } diff --git a/man/clustifyr-package.Rd b/man/clustifyr-package.Rd index 95d3964f..ea1e266a 100644 --- a/man/clustifyr-package.Rd +++ b/man/clustifyr-package.Rd @@ -18,11 +18,11 @@ Useful links: } \author{ -\strong{Maintainer}: Kent Riemondy \email{kent.riemondy@gmail.com} +\strong{Maintainer}: Rui Fu \email{ray.sinensis@gmail.com} Authors: \itemize{ - \item Rui Fu \email{raysinensis@gmail.com} + \item Kent Riemondy \email{kent.riemondy@gmail.com} } Other contributors: diff --git a/man/get_ucsc_reference.Rd b/man/get_ucsc_reference.Rd index 6060aca8..8c1427f2 100644 --- a/man/get_ucsc_reference.Rd +++ b/man/get_ucsc_reference.Rd @@ -27,11 +27,15 @@ Build reference atlases from external UCSC cellbrowsers # many datasets hosted by UCSC have UMI counts in the expression matrix # set if_log = FALSE if the expression matrix has not been natural log transformed -get_ucsc_reference(cb_url = "https://cells.ucsc.edu/?ds=evocell+mus-musculus+marrow", - cluster_col = "Clusters", if_log = FALSE) - -get_ucsc_reference(cb_url = "http://cells.ucsc.edu/?ds=muscle-cell-atlas", - cluster_col = "cell_annotation", - if_log = FALSE) +get_ucsc_reference( + cb_url = "https://cells.ucsc.edu/?ds=evocell+mus-musculus+marrow", + cluster_col = "Clusters", if_log = FALSE +) + +get_ucsc_reference( + cb_url = "http://cells.ucsc.edu/?ds=muscle-cell-atlas", + cluster_col = "cell_annotation", + if_log = FALSE +) } } diff --git a/man/parse_loc_object.Rd b/man/parse_loc_object.Rd index 35c6ba42..45d00384 100644 --- a/man/parse_loc_object.Rd +++ b/man/parse_loc_object.Rd @@ -36,7 +36,7 @@ list of expression, metadata, vargenes, cluster_col info from object more flexible parsing of single cell objects } \examples{ -so <- so_pbmc() +so <- so_pbmc() obj <- parse_loc_object(so) length(obj) }