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dynverse / dyno

Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕
https://dynverse.github.io/dyno
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Error: Column `is_start` can't be converted from integer to logical #49

Closed Eomesodermin closed 5 years ago

Eomesodermin commented 5 years ago

Hi,

I keep getting an error when trying to plot the trajectory on a dim reduction using plot_dimred() function.

below is an example of analysis flow:

raw.data.spleen <- read.table("output/tables/raw_dataframe_Spleen_only.txt") normed.data.spleen <- read.table("output/tables/filtered_dataframe_Spleen_only.txt")

Dyno.spleen.data <- wrap_expression( counts = raw.data.spleen, expression = normed.data.spleen )

answers.spleen <- dynguidelines::answer_questions( multiple_disconnected = NULL, expect_topology = NULL, expected_topology = NULL, n_cells = 3447, n_features = 12236, memory = "8GB", prior_information = NULL, docker = TRUE )

slingshot.spleen <- infer_trajectory(Dyno.spleen.data, method = "dynverse/ti_slingshot:v0.9.9.01", parameters = NULL, give_priors = NULL, seed = set.seed(42), verbose = TRUE)

plot_dimred(slingshot.spleen)

Coloring by milestone Using milestone_percentages from trajectory Error: Column is_start can't be converted from integer to logical

traceback() 13: stop(list(message = "Column is_start can't be converted from integer to logical", call = NULL, cppstack = NULL)) 12: bindrows(x, .id) 11: bind_rows(divergence_regions, extra_divergences) 10: calculate_geodesicdistances(cell_ids = trajectory$cell_ids, milestone_ids = trajectory$milestone_ids, milestone_network = trajectory$milestone_network, milestone_percentages = trajectory$milestone_percentages, divergence_regions = trajectory$divergence_regions, waypoint_cells = waypoint_cells, waypoint_milestone_percentages = waypoint_milestone_percentages) 9: calculate_geodesic_distances(trajectory, waypoint_milestone_percentages = waypoint_milestone_percentages) 8: dynwrap::select_waypoints(trajectory) 7: is.data.frame(x) 6: colnames(waypoints$geodesic_distances) 5: eval_bare(get_expr(quo), get_env(quo)) 4: quasi_label(enquo(expected)) 3: testthat::expect_setequal(cell_positions$cell_id, colnames(waypoints$geodesic_distances)) 2: project_waypoints(trajectory = trajectory, cell_positions = cell_positions, waypoints = waypoints, trajectory_projection_sd = trajectory_projection_sd, color_trajectory = color_trajectory) 1: plot_dimred(slingshot.liver)

rcannood commented 5 years ago

Hello Eomesodermin,

Does the problem also occur when you use the most recent version of the ti_slingshot container ("dynverse/ti_slingshot:v1.0.0.01" or ti_slingshot())? Make sure that dynwrap and dynmethods are also up to date.

Kind regards, Robrecht

rcannood commented 5 years ago

Closing this issue since it is likely already solved. Feel free to respond to this message if it is not.