dynverse / dyno

Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕
https://dynverse.github.io/dyno
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a problem with infer_trajectory #119

Open Hiroki0905 opened 3 years ago

Hiroki0905 commented 3 years ago

Hello I am now in " running the methods" section in "Quick start" and trying "infer_trajectory" function.

an error message below appeared after "infer_trajectory" function was done. the message says "a start-id is required" and Docker test was successful on my RStudio app.

would you tell me How I can solve this.

library(dyno)
library(tidyverse)

data("fibroblast_reprogramming_treutlein")

dataset <- wrap_expression(
  counts = fibroblast_reprogramming_treutlein$counts,
  expression = fibroblast_reprogramming_treutlein$expression
)
 answers <- dynguidelines::answer_questions(
   multiple_disconnected = FALSE, 
   expect_topology = TRUE, 
   expected_topology = "bifurcation", 
   n_cells = 30000, 
   n_features = 2000, 
   time = "16h", 
   memory = "2GB", 
   prior_information = c("start_id", "end_id", "end_n", "start_n", "leaves_n", "groups_n", "features_id", "dimred"), 
   docker = TRUE
  )
guidelines <- dynguidelines::guidelines(answers = answers) 

methods_selected <- guidelines$methods_selected

model <- infer_trajectory(dataset, first(methods_selected),verbose = TRUE)

message in the console

> model <- infer_trajectory(dataset, first(methods_selected),verbose = TRUE)
Error in .method_extract_priors(dataset, method$wrapper$inputs, give_priors) : 
  Prior information start_id is missing from dataset 20210825_144233__data_wrapper__YTF101hDyJ but is required by the method. 
   -> If known, you can add this prior information using add_prior_information(dataset, start_id = <prior>). 
   -> Otherwise, this method cannot be used.
jpcartailler commented 3 years ago

You need to provide a cell ID (barcode) with which the TI method will "start" the trajectory from.