rooting and pseudotime calculation need some work

[zouter]

• Pseudotime for cycles doesn't make any sense, because the non-directed geodesic distances are used

• calculate_pseudotime shouldn't just root the trajectory as it sees fit. The rooting should be done before pseudotime calculation/plotting.

Otherwise, you get things like this:

[rcannood]

Adding a small reproducible example ;) In both rootings, things are going wrong.

Example code

```r library(tidyverse) library(dyno) milestone_ids <- c("W", "X", "Y", "Z", "A", "B", "C") milestone_network <- tribble( ~from, ~to, ~length, ~directed, "W", "X", 2, TRUE, "X", "Y", 4, TRUE, "Y", "W", 3, TRUE, "Y", "Z", 2, TRUE, "A", "B", 1, TRUE, "C", "A", 1, TRUE ) progressions <- milestone_network %>% rowwise() %>% do({ df <- . tibble( cell_id = paste0(df$from, df$to, seq_len(20)), from = df$from, to = df$to, percentage = seq(0, 1, length.out = length(cell_id)) ) }) %>% ungroup() trajectory <- wrap_data( id = "test", cell_ids = unique(progressions$cell_id) ) %>% add_trajectory( milestone_ids = milestone_ids, milestone_network = milestone_network, progressions = progressions ) g1 <- plot_graph(trajectory, label_milestones = TRUE) t2 <- trajectory %>% add_root(root_milestone_id = "W") g2 <- plot_graph( t2, "pseudotime", pseudotime = calculate_pseudotime(t2), label_milestones = TRUE ) + labs(title = "Root W") t3 <- trajectory %>% add_root(root_milestone_id = "Z") g3 <- plot_graph( t3, "pseudotime", pseudotime = calculate_pseudotime(t3), label_milestones = TRUE ) + labs(title = "Root Z") patchwork::wrap_plots(g1, g2, g3) ggsave("~/plot.png", width = 12, height = 4) ```

[zouter]

Okay, I understand. So if you root at Y (or W, X), you only want to Z-Y if necessary, but not the other edges. So only the edges that are not accessible should be swapped