added new error checks (be25cda8) · Commits · github_fork / HdWGCNA

DESCRIPTION

+1 −1

Original line number	Original line	Diff line number	Diff line
	Package: hdWGCNA		Package: hdWGCNA
	Title: hdWGCNA		Title: hdWGCNA
	Version: 0.1.1.9014		Version: 0.1.1.9015
	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")),

NEWS.md

+12 −2

Original line number	Original line	Diff line number	Diff line
	# hdWGCNA 0.1.1.9012 (2022-08-26)		# hdWGCNA 0.1.1.9015 (2022-09-06)
			## Added
			- None

			## Changes
			- New data format check in `MetacellsByGroups` to ensure that the selected slot is present in the selected assay.
			- `SetDatExpr` now backs up to the full dataset if the metacell dataset isn't found.
			- Changed some text to clarify some points in the Module Preservation tutorial.


			# hdWGCNA 0.1.1.9014 (2022-08-26)
	## Added		## Added
	- None		- None

	@@ -6,7 +16,7 @@
	- Bugfix in `ModuleConnectivity` that caused kMEs to be out of order.		- Bugfix in `ModuleConnectivity` that caused kMEs to be out of order.


	# hdWGCNA 0.1.1.9012 (2022-08-25)		# hdWGCNA 0.1.1.9013 (2022-08-25)
	## Added		## Added
	- Tutorial for using SCTransform normalized data.		- Tutorial for using SCTransform normalized data.

R/getters_and_setters.R

+11 −6

Original line number	Original line	Diff line number	Diff line
	@@ -109,14 +109,15 @@ GetMetacellObject <- function(seurat_obj, wgcna_name=NULL){

	# get data from active assay if wgcna_name is not given		# get data from active assay if wgcna_name is not given
	if(is.null(wgcna_name)){wgcna_name <- seurat_obj@misc$active_wgcna}		if(is.null(wgcna_name)){wgcna_name <- seurat_obj@misc$active_wgcna}
			input_class <- class(seurat_obj@misc[[wgcna_name]]$wgcna_metacell_obj)
	if(class(seurat_obj@misc[[wgcna_name]]$wgcna_metacell_obj) == "Seurat"){		if(input_class == "Seurat"){
	return(seurat_obj@misc[[wgcna_name]]$wgcna_metacell_obj)		return(seurat_obj@misc[[wgcna_name]]$wgcna_metacell_obj)
	} else{		} else if(input_class == "character") {
	metacell_location <- seurat_obj@misc[[wgcna_name]]$wgcna_metacell_obj		metacell_location <- seurat_obj@misc[[wgcna_name]]$wgcna_metacell_obj
	return(seurat_obj@misc[[metacell_location]]$wgcna_metacell_obj)		return(seurat_obj@misc[[metacell_location]]$wgcna_metacell_obj)
			} else{
			return(NULL)
	}		}

	}		}

	############################		############################
	@@ -197,10 +198,14 @@ SetDatExpr <- function(
	genes_use <- GetWGCNAGenes(seurat_obj, wgcna_name)		genes_use <- GetWGCNAGenes(seurat_obj, wgcna_name)
	modules <- GetModules(seurat_obj, wgcna_name)		modules <- GetModules(seurat_obj, wgcna_name)

			# get metacell object
			m_obj <- GetMetacellObject(seurat_obj, wgcna_name)

	# use metacells or whole seurat object?		# use metacells or whole seurat object?
	if(use_metacells){		if(use_metacells & !is.null(m_obj)){
	s_obj <- GetMetacellObject(seurat_obj, wgcna_name)		s_obj <- m_obj
	} else{		} else{
			if(is.null(m_obj)){warning("Metacell Seurat object not found. Using full Seurat object instead.")}
	s_obj <- seurat_obj		s_obj <- seurat_obj
	}		}

R/metacells.R

+12 −0

Original line number	Original line	Diff line number	Diff line
	@@ -261,6 +261,18 @@ MetacellsByGroups <- function(
	stop(paste0('Assay ', assay, ' not found in seurat_obj. Select a valid assay: ', paste0(names(seurat_obj@assays), collapse = ', ')))		stop(paste0('Assay ', assay, ' not found in seurat_obj. Select a valid assay: ', paste0(names(seurat_obj@assays), collapse = ', ')))
	}		}

			# check slot:
			if(!(slot %in% c('counts', 'data', 'scale.data'))){
			stop('Invalid input for slot. Valid choices are counts, data, scale.data.')
			} else{

			# check the shape of the slot
			slot_dim <- dim(GetAssayData(seurat_obj, assay=assay, slot=slot))
			if(any(slot_dim) == 0){
			stop(paste(c("Selected slot ", slot, " not found in this assay.")))
			}
			}

	# subset seurat object by seleted cells:		# subset seurat object by seleted cells:
	if(!is.null(cells.use)){		if(!is.null(cells.use)){
	seurat_full <- seurat_obj		seurat_full <- seurat_obj

docs/404.html

+1 −1

Original line number	Original line	Diff line number	Diff line
	@@ -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="">0.1.1.9014</span>		<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1.9015</span>
	</span>		</span>
	</div>		</div>

Admin message