## Render multiple fast GSEA reports.
## Updated 2022-05-24.
## nolint start
suppressPackageStartupMessages({
library(rmarkdown)
})
## nolint end
templateFile <- "fgsea.Rmd"
stopifnot(file.exists(templateFile))
## Load the FgseaList objects.
datasets <- c(
"name1" = "fgsealist1",
"name2" = "fgsealist2"
)
objectFiles <- file.path(
"rds",
Sys.Date(),
paste0(datasets, ".rds")
)
names(objectFiles) <- names(datasets)
stopifnot(all(file.exists(objectFiles)))
outputDir <- file.path("results", Sys.Date(), "fgsea")
invisible(Map(
name = names(objectFiles),
file = objectFiles,
f = function(name, file) {
message(sprintf(
"Rendering '%s'\nFile: %s",
name, file
))
render(
params = list(
title = paste("GSEA:", name),
object = file,
name = name,
output_dir = outputDir
),
input = templateFile,
output_format = "html_document",
output_file = paste0(name, ".html"),
output_dir = outputDir,
clean = TRUE,
envir = new.env()
)
}
))
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