After running cellTypeAssignSCRNA I have 12 clusters of single cells with the CDSeq estimates assigned to specific clusters. Currently the clusters have generic labeling (i.e., cluster_0, cluster_1, ...) but after reviewing each clusters marker genes I would like to assign meaningful cell type labels (i.e, endothelial cells, monocytes,...) for each cluster. I am not sure if the umap and tsne ggplot are able to be edited after running cellTypeAssignSCRNA. Renaming cluster labels in the plot environment as shown below will change this data slot in the result but will not change the output of the umap plot.
levels(cdseq.result.celltypeassign[["cdseq_scRNA_umap"]][["plot_env"]][["cluster_label"]]) <- new.cluster.ids
Any suggestions are greatly appreciated.
After running cellTypeAssignSCRNA I have 12 clusters of single cells with the CDSeq estimates assigned to specific clusters. Currently the clusters have generic labeling (i.e., cluster_0, cluster_1, ...) but after reviewing each clusters marker genes I would like to assign meaningful cell type labels (i.e, endothelial cells, monocytes,...) for each cluster. I am not sure if the umap and tsne ggplot are able to be edited after running cellTypeAssignSCRNA. Renaming cluster labels in the plot environment as shown below will change this data slot in the result but will not change the output of the umap plot.
levels(cdseq.result.celltypeassign[["cdseq_scRNA_umap"]][["plot_env"]][["cluster_label"]]) <- new.cluster.idsAny suggestions are greatly appreciated.