Bud fixes (01474202) · Commits · github_fork / Plot1cell

R/plot_dot.R

+4 −2

Original line number	Original line	Diff line number	Diff line
	@@ -27,18 +27,20 @@ complex_dotplot_single <- function(
	do.scale=T,		do.scale=T,
	scale.by='radius'		scale.by='radius'
	){		){
			seu_obj@meta.data[,groupby]<-gsub("_","-",seu_obj@meta.data[,groupby])
	if (is.null(levels(seu_obj@meta.data[,groupby]))){		if (is.null(levels(seu_obj@meta.data[,groupby]))){
	seu_obj@meta.data[,groupby] <-factor(seu_obj@meta.data[,groupby], levels = names(table(seu_obj@meta.data[,groupby])))		seu_obj@meta.data[,groupby] <-factor(seu_obj@meta.data[,groupby], levels = names(table(seu_obj@meta.data[,groupby])))
	}		}
	groupby_level<-levels(seu_obj@meta.data[,groupby])		groupby_level<-levels(seu_obj@meta.data[,groupby])
	levels(seu_obj)<-rev(levels(seu_obj))		levels(seu_obj)<-rev(levels(seu_obj))
	celltypes<-levels(seu_obj)		celltypes<-levels(seu_obj)
	celltypes<-gsub("_", ".", celltypes)		celltypes<-gsub("_", "-", celltypes)
	seu_obj@meta.data$celltype<-as.character(seu_obj@active.ident)		seu_obj@meta.data$celltype<-as.character(seu_obj@active.ident)
	seu_obj@meta.data$celltype<-gsub("_", ".", seu_obj@meta.data$celltype)		seu_obj@meta.data$celltype<-gsub("_", "-", seu_obj@meta.data$celltype)
	seu_obj<-SetIdent(seu_obj, value='celltype')		seu_obj<-SetIdent(seu_obj, value='celltype')
	levels(seu_obj)<-celltypes		levels(seu_obj)<-celltypes
	if(!is.null(splitby)){		if(!is.null(splitby)){
			seu_obj@meta.data[,splitby]<-gsub("_","-",seu_obj@meta.data[,splitby])
	if (is.null(levels(seu_obj@meta.data[,splitby]))){		if (is.null(levels(seu_obj@meta.data[,splitby]))){
	seu_obj@meta.data[,splitby] <-factor(seu_obj@meta.data[,splitby], levels = names(table(seu_obj@meta.data[,splitby])))		seu_obj@meta.data[,splitby] <-factor(seu_obj@meta.data[,splitby], levels = names(table(seu_obj@meta.data[,splitby])))
	}		}

R/utils.R

+3 −1

Original line number	Original line	Diff line number	Diff line
	@@ -356,7 +356,9 @@ extract_gene_count <- function(
	if(is.null(meta.groups)){		if(is.null(meta.groups)){
	meta.groups=colnames(seu@meta.data)		meta.groups=colnames(seu@meta.data)
	}		}
			if(!is.null(cell.types)){
	new_seu<-subset(seu, idents=cell.types)		new_seu<-subset(seu, idents=cell.types)
			}
	feature_count<-Seurat::FetchData(new_seu, slot = data.type, vars = c(features,meta.groups,"celltype"))		feature_count<-Seurat::FetchData(new_seu, slot = data.type, vars = c(features,meta.groups,"celltype"))
	umap_data<-data.frame(new_seu[["umap"]]@cell.embeddings)		umap_data<-data.frame(new_seu[["umap"]]@cell.embeddings)
	feature_count$UMAP1<-umap_data$UMAP_1		feature_count$UMAP1<-umap_data$UMAP_1

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