inst/hicli.R

In hiplot/hiplotlib: Native Plugin Backend of Hiplot Platform

#!/usr/bin/env Rscript

suppressPackageStartupMessages(library(optparse))
suppressPackageStartupMessages(library(hiplotlib))

initial_options <- commandArgs(trailingOnly = FALSE)

file_arg_name <- "--file="
script_name <- sub(
  file_arg_name, "",
  initial_options[grep(file_arg_name, initial_options)]
)

# Options
option_list <- list(
  make_option(c("-i", "--inputFile"),
    default = "",
    help = "input data"
  ),
  make_option(c("-c", "--confFile"),
    default = "",
    help = "configuration file"
  ),
  make_option(c("-o", "--outputFilePrefix"),
    default = "",
    help = "prefix of output plots"
  ),
  make_option(c("-t", "--tool"),
    default = "heatmap",
    help = "(e.g. heatmap))"
  ),
  make_option(c("-m", "--module"),
    default = "basic",
    help = "module name (e.g. basic)"
  ),
  make_option(c("-s", "--simple"),
    default = FALSE,
    action = "store_true",
    help = "only source core.R"
  ),
  make_option(c("-e", "--enableExample"),
    default = FALSE,
    action = "store_true",
    help = "enable auto load example"
  )
)

opt <- parse_args(OptionParser(option_list = option_list))
# print(dput(opt))
# quit("no")

if (file.exists(file.path(dirname(opt$confFile), "plot.R"))) {
  message("Running from developer mode")
  script_dir <<- dirname(normalizePath(dirname(opt$confFile)))
} else {
  message("Running from server mode")
  script_dir <<- dirname(script_name)
}

ow <- getwd()
renv_dir <- file.path(script_dir, "../../")
# TODO 这个用一个option去控制是否更好？
if (file.exists(file.path(renv_dir, ".Rprofile"))) {
  setwd(renv_dir)
  source(".Rprofile")
}
setwd(ow)

if (!opt$simple) {
  set_extra_pkgs()
}

outlog_dir <- file.path(dirname(opt$outputFilePrefix), "log")
if (!dir.exists(outlog_dir)) {
  dir.create(outlog_dir, recursive = TRUE, showWarnings = TRUE)
}
run_hiplot()