I have a question regarding pseudotime analysis. It seems, this analysis is done over only a certain cell type. However, I am wondering if we can apply it on all the cells we got from UMAP out of single-cell analysis. Can we? Also, If we want to apply it only on a certain cell type or possibly cells with a cell ancestor, when we want to select them, how we can do it? In Monocle3, in "oder_cells" command, there is a pop up window and then we can select one cell as a root cell. However, when I do this, it still applied the pseudotime over all cells in the UMAP but I see in literature that for the pseudotime result, there is only a figure that shows pseudotime result with only selected cells not all cells in the analysis. I am wondering how we can do this?
