#!/usr/local/bin/Rscript
task <- dyncli::main()
# load libraries
library(dyncli, warn.conflicts = FALSE)
library(dynwrap, warn.conflicts = FALSE)
library(dplyr, warn.conflicts = FALSE)
library(purrr, warn.conflicts = FALSE)
library(TEMPLATE)
#####################################
### LOAD DATA ###
#####################################
expression <- task$expression
params <- task$params
priors <- task$priors
# TIMING: done with preproc
timings <- list(method_afterpreproc = Sys.time())
#####################################
### INFER TRAJECTORY ###
#####################################
# do TI calculations
# TIMING: done with trajectory inference
timings$method_aftermethod <- Sys.time()
#####################################
### SAVE OUTPUT TRAJECTORY ###
#####################################
output <-
wrap_data(
cell_ids = rownames(expression)
) %>%
add_dimred(
dimred = dimred
) %>%
add_cell_graph(
cell_graph = cell_graph,
to_keep = to_keep
) %>%
add_timings(
timings = timings
)
dyncli::write_output(output, task$output)
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