Loading DESCRIPTION +1 −1 Original line number Original line Diff line number Diff line Package: hdWGCNA Package: hdWGCNA Title: hdWGCNA Title: hdWGCNA Version: 0.1.1.9013 Version: 0.1.1.9014 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 +8 −0 Original line number Original line Diff line number Diff line # hdWGCNA 0.1.1.9012 (2022-08-26) ## Added - None ## Changes - Bugfix in `ModuleConnectivity` that caused kMEs to be out of order. # hdWGCNA 0.1.1.9012 (2022-08-25) # hdWGCNA 0.1.1.9012 (2022-08-25) ## Added ## Added - Tutorial for using SCTransform normalized data. - Tutorial for using SCTransform normalized data. Loading R/WGCNA_functions.R +4 −1 Original line number Original line Diff line number Diff line Loading @@ -962,8 +962,11 @@ ModuleConnectivity <- function( # add module color to the kMEs table # add module color to the kMEs table modules <- modules[,1:3] modules <- modules[,1:3] mods <- levels(modules$module) colnames(kMEs) <- colnames(MEs) kMEs <- kMEs[,mods] colnames(kMEs) <- paste0("kME_", colnames(kMEs)) kMEs <- cbind(modules, kMEs) kMEs <- cbind(modules, kMEs) colnames(kMEs) <- c(colnames(modules), paste0("kME_", colnames(MEs))) # update the modules table in the Seurat object: # update the modules table in the Seurat object: seurat_obj <- SetModules(seurat_obj, kMEs, wgcna_name) seurat_obj <- SetModules(seurat_obj, kMEs, wgcna_name) Loading R/getters_and_setters.R +20 −2 Original line number Original line Diff line number Diff line Loading @@ -1203,8 +1203,27 @@ ResetModuleNames <- function( # get modules # get modules modules <- GetModules(seurat_obj, wgcna_name) modules <- GetModules(seurat_obj, wgcna_name) old_mods <- levels(modules$module) old_mods <- levels(modules$module) nmods <- length(old_mods) - 1 # if it's a named list: if(class(new_name) == 'list'){ if(all(names(new_name) %in% old_mods)){ ix <- match(names(new_name), old_mods) new_names <- old_mods new_names[ix] <- as.character(new_name) new_names <- new_names[new_names != 'grey'] } else{ stop("Some module names present in new_name are not found in this hdWGCNA experiment.") } } else if(length(new_name) == 1){ new_names <- paste0(new_name, 1:nmods) } else if(length(new_name) == nmods){ new_names <- new_name } else{ stop("Invalid input for new_name.") } new_names <- paste0(new_name, 1:(length(old_mods)-1)) grey_ind <- which(old_mods == 'grey') grey_ind <- which(old_mods == 'grey') # account for when grey is first / last # account for when grey is first / last Loading Loading @@ -1352,7 +1371,6 @@ ResetModuleColors <- function( # case where we give a named list: # case where we give a named list: if(class(new_colors) == 'list'){ if(class(new_colors) == 'list'){ print('named list') ix <- match(names(new_colors), mod_colors_df$module) ix <- match(names(new_colors), mod_colors_df$module) mod_colors_df[ix, 'color'] <- as.character(new_colors) mod_colors_df[ix, 'color'] <- as.character(new_colors) new_colors <- mod_colors_df$color new_colors <- mod_colors_df$color Loading docs/404.html +1 −1 Original line number Original line Diff line number Diff line Loading @@ -39,7 +39,7 @@ </button> </button> <span class="navbar-brand"> <span class="navbar-brand"> <a class="navbar-link" href="https://smorabit.github.io/hdWGCNA/index.html">hdWGCNA</a> <a class="navbar-link" href="https://smorabit.github.io/hdWGCNA/index.html">hdWGCNA</a> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1.9013</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1.9014</span> </span> </span> </div> </div> Loading Loading
DESCRIPTION +1 −1 Original line number Original line Diff line number Diff line Package: hdWGCNA Package: hdWGCNA Title: hdWGCNA Title: hdWGCNA Version: 0.1.1.9013 Version: 0.1.1.9014 Authors@R: c( Authors@R: c( person("Sam", "Morabito", , "smorabit@uci.edu", role = c("aut", "cre"), person("Sam", "Morabito", , "smorabit@uci.edu", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7768-4856")), comment = c(ORCID = "0000-0002-7768-4856")), Loading
NEWS.md +8 −0 Original line number Original line Diff line number Diff line # hdWGCNA 0.1.1.9012 (2022-08-26) ## Added - None ## Changes - Bugfix in `ModuleConnectivity` that caused kMEs to be out of order. # hdWGCNA 0.1.1.9012 (2022-08-25) # hdWGCNA 0.1.1.9012 (2022-08-25) ## Added ## Added - Tutorial for using SCTransform normalized data. - Tutorial for using SCTransform normalized data. Loading
R/WGCNA_functions.R +4 −1 Original line number Original line Diff line number Diff line Loading @@ -962,8 +962,11 @@ ModuleConnectivity <- function( # add module color to the kMEs table # add module color to the kMEs table modules <- modules[,1:3] modules <- modules[,1:3] mods <- levels(modules$module) colnames(kMEs) <- colnames(MEs) kMEs <- kMEs[,mods] colnames(kMEs) <- paste0("kME_", colnames(kMEs)) kMEs <- cbind(modules, kMEs) kMEs <- cbind(modules, kMEs) colnames(kMEs) <- c(colnames(modules), paste0("kME_", colnames(MEs))) # update the modules table in the Seurat object: # update the modules table in the Seurat object: seurat_obj <- SetModules(seurat_obj, kMEs, wgcna_name) seurat_obj <- SetModules(seurat_obj, kMEs, wgcna_name) Loading
R/getters_and_setters.R +20 −2 Original line number Original line Diff line number Diff line Loading @@ -1203,8 +1203,27 @@ ResetModuleNames <- function( # get modules # get modules modules <- GetModules(seurat_obj, wgcna_name) modules <- GetModules(seurat_obj, wgcna_name) old_mods <- levels(modules$module) old_mods <- levels(modules$module) nmods <- length(old_mods) - 1 # if it's a named list: if(class(new_name) == 'list'){ if(all(names(new_name) %in% old_mods)){ ix <- match(names(new_name), old_mods) new_names <- old_mods new_names[ix] <- as.character(new_name) new_names <- new_names[new_names != 'grey'] } else{ stop("Some module names present in new_name are not found in this hdWGCNA experiment.") } } else if(length(new_name) == 1){ new_names <- paste0(new_name, 1:nmods) } else if(length(new_name) == nmods){ new_names <- new_name } else{ stop("Invalid input for new_name.") } new_names <- paste0(new_name, 1:(length(old_mods)-1)) grey_ind <- which(old_mods == 'grey') grey_ind <- which(old_mods == 'grey') # account for when grey is first / last # account for when grey is first / last Loading Loading @@ -1352,7 +1371,6 @@ ResetModuleColors <- function( # case where we give a named list: # case where we give a named list: if(class(new_colors) == 'list'){ if(class(new_colors) == 'list'){ print('named list') ix <- match(names(new_colors), mod_colors_df$module) ix <- match(names(new_colors), mod_colors_df$module) mod_colors_df[ix, 'color'] <- as.character(new_colors) mod_colors_df[ix, 'color'] <- as.character(new_colors) new_colors <- mod_colors_df$color new_colors <- mod_colors_df$color Loading
docs/404.html +1 −1 Original line number Original line Diff line number Diff line Loading @@ -39,7 +39,7 @@ </button> </button> <span class="navbar-brand"> <span class="navbar-brand"> <a class="navbar-link" href="https://smorabit.github.io/hdWGCNA/index.html">hdWGCNA</a> <a class="navbar-link" href="https://smorabit.github.io/hdWGCNA/index.html">hdWGCNA</a> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1.9013</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1.9014</span> </span> </span> </div> </div> Loading
