#' @importFrom utils write.csv2
run_meta_report <- function(...) {
# Simulate some data and put it into a CSV file
sim_data <- SimulateGMCMData(n = 1000, par = c(pie1 = 0.3, mu = 2,
sigma = 1.1, rho = 0.2))$z
colnames(sim_data) <- c("u133", "exon")
data_file <- tempfile()
utils::write.csv2(sim_data, file = data_file)
# GENERAL GMCM ----
report_path_full <- system.file("shiny", "www", "report_full.Rmd",
package = "GMCM", lib.loc = .libPaths()[1],
mustWork = TRUE)
# Parameters to expand
params <- list(data_file = data_file,
header = TRUE,
sep = ";",
quote = '\"',
model_cols = c("u133", "exon"),
theta = GMCM::rtheta(m = 2, d = 2),
fit_method = "NM",
max_ite = 50,
full_class_type = "thres_prob",
full_thres_prob = 0.9)
expand_args <- c(list(file = report_path_full), params)
report_expanded <- do.call(knitr::knit_expand, expand_args)
# Write to temp file
report_expanded_path <- tempfile()
cat(report_expanded, file = report_expanded_path)
# We can purl
res3 <- knitr::purl(report_expanded_path,
output = paste0(report_expanded_path, ".R"),
documentation = 0)
# Render the expanded document
res4 <- rmarkdown::render(
input = report_expanded_path,
output_options = list(self_contained = TRUE),
envir = new.env(parent = globalenv())
)
return(invisible(list(report_expanded_path, res3, res4)))
}
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