error checking (b4842b7c) · Commits · github_fork / HdWGCNA

DESCRIPTION

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		Package: hdWGCNA
		Title: hdWGCNA
		Version: 0.2.02
		Version: 0.2.03
		Authors@R: c(
		person("Sam", "Morabito", , "smorabit@uci.edu", role = c("aut", "cre"),
		comment = c(ORCID = "0000-0002-7768-4856")),

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		# hdWGCNA 0.2.03 (2022-11-010)
		## Added
		- None

		## Changes
		- New error checking in `MetaspotsByGroups`
		- `MetacellsByGroups` now keeps track of which cells were merged.


		# hdWGCNA 0.2.02 (2022-11-01)
		## Added
		- None

+14 −2

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		@@ -31,7 +31,19 @@ ConstructMetaspots <- function(

		# loop boundaries
		col_bounds <- col_range[1]:col_range[2]

		if(length(col_bounds) >= 4){
		col_bounds <- col_bounds[which(1:length(col_bounds) %% 4 == 0)]
		} else if(length(col_bounds) == 3){
		warning('The selected grouping is spatially constrained and might fail the metaspot aggregation step. You may wish to change the group.by parameter to form larger groups.')
		col_bounds <- col_bounds[2]
		} else if(length(col_bounds) >= 1){
		warning('The selected grouping is spatially constrained and might fail the metaspot aggregation step. You may wish to change the group.by parameter to form larger groups.')
		col_bounds <- col_bounds[1]
		} else{
		warning('No columns specified. Need to change the group.by parameter.')
		return()
		}

		# even or odd cols?
		if(all(col_bounds %% 2 == 0)){even = TRUE} else{even = FALSE}
		@@ -102,7 +114,6 @@ ConstructMetaspots <- function(
		})

		if(length(tmp) <= 1){
		print('here')
		next
		}

		@@ -130,6 +141,7 @@ ConstructMetaspots <- function(

		# combine expression results
		if(length(tmp) <= 1){
		warning('Metaspot aggregation failed for this grouping.')
		return(NULL)
		}
		agg_X <- do.call(rbind, lapply(1:length(tmp), function(k){tmp[[k]][[3]]}))

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		@@ -108,6 +108,10 @@ MetaspotsByGroups <- function(
		metaspot_list <- metaspot_list[-remove]
		}

		if(length(metaspot_list) == 0){
		stop('All metaspot aggregations failed.')
		}

		# combine density information:
		if(length(metaspot_list) > 1){
		density_agg <- unlist(lapply(metaspot_list, function(x){x@misc$density_agg}))

+8 −1

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		@@ -92,6 +92,11 @@ ConstructMetacells <- function(
		#
		# combs <- combn(nrow(cell_sample), 2)

		# get a list of the cell barcodes that have been merged:
		cells_merged <- apply(cell_sample, 1, function(x){
		paste0(colnames(seurat_obj)[x], collapse=',')
		})

		combs <- tryCatch(
		{combn(nrow(cell_sample), 2)},
		error = function(cond){return(NA)}
		@@ -101,7 +106,6 @@ ConstructMetacells <- function(
		return(NULL)
		}


		shared <- apply(combs, 2, function(x) {
		k2 - length(unique(as.vector(cell_sample[x, ])))
		})
		@@ -148,6 +152,9 @@ ConstructMetacells <- function(
		)
		}

		# add the cells merged info to the metacell obj
		metacell_obj$cells_merged <- as.character(cells_merged)

		# calculate stats:
		# shared <- shared[shared <= max_shared]
		max_shared <- max(shared)