root cell or milestone not provided, trying first outgoing milestone_id

[grimwoo]

thanks for developing such a magnificent software . here i encounter a problem : i set one cell as root (start ) according to tutorial model_rooted <- model %>% add_root(root_cell_id = Root.cell.id). However, i still got the warning information, Coloring by grouping root cell or milestone not provided, trying first outgoing milestone_id Using 'milestone_begin' as root with the plot that the root cell possessed high pseudotime (which means i failed in setting root cell), while using plot_dimred(model_rooted, expression_source = dataset$expression, grouping = dataset$grouping, dimred = dataset$dimred).

Background i already set the start for dataset

  dataset <- wrap_expression(
    expression = t(as.matrix(Patient.object@[email protected])),
    counts = t(as.matrix(Patient.object@assays$RNA@counts))
  )
  groups_id <- matrix(nrow = length([email protected]$Final_cluster), ncol = 2)
  colnames(groups_id) <- c('cell_id','group_id')
  groups_id[,1] <-  rownames([email protected])
  groups_id[,2] <-  Patient.object$Final_cluster
  dataset <- add_grouping(
    dataset = dataset,
    as.data.frame(groups_id)
  )
  dataset <- add_grouping(
    dataset,
    Patient.object$Final_cluster
  )
  dataset <- add_dimred(
    dataset,
    Patient.object@[email protected]
  )
    Patient.object.subset <- subset(x = Patient.object, subset = Final_cluster == 'Stem_cells')
  dataset <- add_prior_information(
  dataset,
  start_id = rownames([email protected])
)

moreover , could you please let me know the better way to set a group of cells as "start"?

[grimwoo]

moreover, even though i set the glaucous cells ( marked by red boxes and arrows) as the start cells, the trejactory and pseudotime still did not start at them.