plot_network_graph() only plot target genes

[zhenzuo2]

Hi,

The dimension of seurat_object@grn@networks$glm_network@graphs$umap_graph is the same as number of target genes saved in seurat_object@grn@networks$glm_network.

As a result, only TFs that are also target genes were plotted. Is this an undocumented feature?

Thanks.

[joschif]

Yes, this is true for the umap layout, since here genes are represented by their regulators in the GRN. If you use another (e.g. forece-directed) layout for the GRN then Pando keeps all genes