Nothing
## ----setup--------------------------------------------------------------------
library(dynwrap)
# dyncli is not installed on travis or CRAN, so don't run some parts of the vignette there
NOT_CRAN <- Sys.getenv("NOT_CRAN") == "" || identical(tolower(Sys.getenv("NOT_CRAN")), "true")
NOT_TRAVIS <- !identical(tolower(Sys.getenv("TRAVIS")), "true")
## -----------------------------------------------------------------------------
definition <- definition(
method = def_method(
id = "comp1"
),
parameters = def_parameters(
dynparam::integer_parameter(
id = "component",
default = 1,
distribution = dynparam::uniform_distribution(1, 10),
description = "The nth component to use"
)
),
wrapper = def_wrapper(
input_required = "expression",
input_optional = "start_id"
)
)
## -----------------------------------------------------------------------------
run_fun <- function(expression, priors, parameters, seed, verbose) {
pca <- prcomp(expression)
pseudotime <- pca$x[, parameters$component]
# flip pseudotimes using start_id
if (!is.null(priors$start_id)) {
if(mean(pseudotime[start_id]) > 0.5) {
pseudotime <- 1-pseudotime
}
}
dynwrap::wrap_data(cell_ids = rownames(expression)) %>%
dynwrap::add_linear_trajectory(pseudotime = pseudotime)
}
## -----------------------------------------------------------------------------
ti_comp1 <- create_ti_method_r(definition, run_fun, package_loaded = "dplyr")
## -----------------------------------------------------------------------------
dataset <- dynwrap::example_dataset
trajectory <- infer_trajectory(dataset, ti_comp1())
## ---- eval=FALSE--------------------------------------------------------------
# library(dynplot)
# # for now, install from github using:
# # remotes::install_github("dynverse/dynplot")
# plot_graph(trajectory)
# plot_heatmap(trajectory, expression_source = dataset$expression)
## -----------------------------------------------------------------------------
#' Infer a trajectory from the first principal component
#'
#' @eval dynwrap::generate_parameter_documentation(definition)
#'
#' @import dplyr
#' @export
#'
#' @examples
#' dataset <- dynwrap::example_dataset
#' model <- dynwrap::infer_trajectory(dataset, ti_comp1())
ti_comp1 <- create_ti_method_r(definition, run_fun)
## -----------------------------------------------------------------------------
generate_parameter_documentation(definition)
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