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# select cells without "melanoma" in the combined_clusters col
subdata<-data[, !grepl("melanoma", data@meta.data$combined_clusters)]
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but if we check the levels of subdata, cells with “melanoma” are stil in
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table(subdata$combined_clusters)
CAFs immune 1 keratinocytes 3
195 162 127
immune 2 melanoma mesenchymal
106 0
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this will cause error if we run RCTD:
process_cell_type_info error: need a minimum of 25 cells for each cell type in the reference
solution 1: set combined_clusters as default Idents of subdata
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subdata<-SetIdent(subdata, value = subdata$combined_clusters)
levels(subdata@active.ident)
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solution 2: drop levels
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subdata$combined_clusters<-droplevels(subdata$combined_clusters, exclude=c("melanoma mesenchymal"))
table(subdata$combined_clusters)
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DefaultAssay(SeuObj)<-"RNA"
SeuObj<-SetIdent(SeuObj, value=SeuObj@meta.data[["colname"]])
deg<-FindAllMarkers(SeuObj)
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rename clusters
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new_cluster.ids<-c("late germ cells", "intermediate germ cells", "GSC/GSC progeny")
names(x=new_cluster.ids)<-levels(x=SeuObj)
SeuObj <- RenameIdents(object = SeuObj, new_cluster.ids)
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SeuObj$new_col<-dataframe$col2merge[match(rownames(SeuObj@meta.data), rownames(dataframe))]
# or cbind if rownames are in the same order
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DimPlot and FeaturePlot
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# DimPlot on another col
DimPlot(SeuObj, group.by="colname", cols=myCol)
# FeaturePlot
FeaturePlot(SeuObj, features="colname", split.by="groupname")+scale_colour_gradientn(colours=brewer.pal(n=9, name="YlOrRd"))
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change NAs in col to “ambiguous”
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SeuObj$colname[which(is.na(SeuObj$colname))]<-"ambiguous"
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# add raw count to metadata
SeuObj$Sox10<-SeuObj@assays$RNA@counts["Sox10",]
# correlation scatter
ggplot(SeuObj@meta.data, aes(colname, Sox10))+geom_point()
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eg. compare cell annotation results or different res
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meta.sel<-SeuObj@meta.data[, c("col1", "col2")]
sankeyform<-highcharter::data_to_sankey(meta.sel)
ggplot(as.data.frame(sankeyform), aes(y=weight, axis1=from, axis2=to))+geom_flow(aes(fill=from, na.rm=FALSE), width=1/3)+
geom_stratum(width=1/3)+geom_text(stat="stratum", aes(label=after_stat(stratum), size=3, color="blue"))+guides(fill="none")
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