Loading DESCRIPTION +1 −1 Original line number Original line Diff line number Diff line Package: hdWGCNA Package: hdWGCNA Title: hdWGCNA Title: hdWGCNA Version: 0.1.1.9012 Version: 0.1.1.9013 Authors@R: c( Authors@R: c( person("Sam", "Morabito", , "smorabit@uci.edu", role = c("aut", "cre"), person("Sam", "Morabito", , "smorabit@uci.edu", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7768-4856")), comment = c(ORCID = "0000-0002-7768-4856")), Loading NEWS.md +9 −1 Original line number Original line Diff line number Diff line # hdWGCNA 0.1.1.9012 (2022-08-27) # hdWGCNA 0.1.1.9012 (2022-08-25) ## Added - Tutorial for using SCTransform normalized data. ## Changes - None # hdWGCNA 0.1.1.9012 (2022-08-24) ## Added ## Added - None - None Loading R/getters_and_setters.R +0 −1 Original line number Original line Diff line number Diff line Loading @@ -207,7 +207,6 @@ SetDatExpr <- function( # get the metadata from the seurat object: # get the metadata from the seurat object: seurat_meta <- s_obj@meta.data seurat_meta <- s_obj@meta.data if(is.null(assay)){ if(is.null(assay)){ assay <- DefaultAssay(s_obj) assay <- DefaultAssay(s_obj) warning(paste0('assay not specified, trying to use assay ', assay)) warning(paste0('assay not specified, trying to use assay ', assay)) Loading R/metacells.R +0 −3 Original line number Original line Diff line number Diff line Loading @@ -316,7 +316,6 @@ MetacellsByGroups <- function( ) ) names(metacell_list) <- groupings names(metacell_list) <- groupings print('done making metacells') # remove NULL # remove NULL remove <- which(sapply(metacell_list, is.null)) remove <- which(sapply(metacell_list, is.null)) Loading @@ -332,14 +331,12 @@ MetacellsByGroups <- function( } } # combine metacell objects # combine metacell objects print(length(metacell_list)) if(length(metacell_list) > 1){ if(length(metacell_list) > 1){ metacell_obj <- merge(metacell_list[[1]], metacell_list[2:length(metacell_list)]) metacell_obj <- merge(metacell_list[[1]], metacell_list[2:length(metacell_list)]) } else{ } else{ metacell_obj <- metacell_list[[1]] metacell_obj <- metacell_list[[1]] } } print('metacell shape') # set idents for metacell object: # set idents for metacell object: Loading _pkgdown.yml +2 −0 Original line number Original line Diff line number Diff line Loading @@ -62,6 +62,8 @@ navbar: - text: Other - text: Other - text: Module customization - text: Module customization href: articles/customization.html href: articles/customization.html - text: Using SCTransform normalized data href: articles/sctransform.html - text: ------- - text: ------- - text: All vignettes - text: All vignettes href: articles/index.html href: articles/index.html Loading Loading
DESCRIPTION +1 −1 Original line number Original line Diff line number Diff line Package: hdWGCNA Package: hdWGCNA Title: hdWGCNA Title: hdWGCNA Version: 0.1.1.9012 Version: 0.1.1.9013 Authors@R: c( Authors@R: c( person("Sam", "Morabito", , "smorabit@uci.edu", role = c("aut", "cre"), person("Sam", "Morabito", , "smorabit@uci.edu", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7768-4856")), comment = c(ORCID = "0000-0002-7768-4856")), Loading
NEWS.md +9 −1 Original line number Original line Diff line number Diff line # hdWGCNA 0.1.1.9012 (2022-08-27) # hdWGCNA 0.1.1.9012 (2022-08-25) ## Added - Tutorial for using SCTransform normalized data. ## Changes - None # hdWGCNA 0.1.1.9012 (2022-08-24) ## Added ## Added - None - None Loading
R/getters_and_setters.R +0 −1 Original line number Original line Diff line number Diff line Loading @@ -207,7 +207,6 @@ SetDatExpr <- function( # get the metadata from the seurat object: # get the metadata from the seurat object: seurat_meta <- s_obj@meta.data seurat_meta <- s_obj@meta.data if(is.null(assay)){ if(is.null(assay)){ assay <- DefaultAssay(s_obj) assay <- DefaultAssay(s_obj) warning(paste0('assay not specified, trying to use assay ', assay)) warning(paste0('assay not specified, trying to use assay ', assay)) Loading
R/metacells.R +0 −3 Original line number Original line Diff line number Diff line Loading @@ -316,7 +316,6 @@ MetacellsByGroups <- function( ) ) names(metacell_list) <- groupings names(metacell_list) <- groupings print('done making metacells') # remove NULL # remove NULL remove <- which(sapply(metacell_list, is.null)) remove <- which(sapply(metacell_list, is.null)) Loading @@ -332,14 +331,12 @@ MetacellsByGroups <- function( } } # combine metacell objects # combine metacell objects print(length(metacell_list)) if(length(metacell_list) > 1){ if(length(metacell_list) > 1){ metacell_obj <- merge(metacell_list[[1]], metacell_list[2:length(metacell_list)]) metacell_obj <- merge(metacell_list[[1]], metacell_list[2:length(metacell_list)]) } else{ } else{ metacell_obj <- metacell_list[[1]] metacell_obj <- metacell_list[[1]] } } print('metacell shape') # set idents for metacell object: # set idents for metacell object: Loading
_pkgdown.yml +2 −0 Original line number Original line Diff line number Diff line Loading @@ -62,6 +62,8 @@ navbar: - text: Other - text: Other - text: Module customization - text: Module customization href: articles/customization.html href: articles/customization.html - text: Using SCTransform normalized data href: articles/sctransform.html - text: ------- - text: ------- - text: All vignettes - text: All vignettes href: articles/index.html href: articles/index.html Loading
