R/zzz.R

In heatmaply: Interactive Cluster Heat Maps Using 'plotly' and 'ggplot2'

# Copyright (C) Tal Galili
#
# This file is part of heatmaply.
#
# heatmaply is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
# heatmaply is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
#  A copy of the GNU General Public License is available at
#  http://www.r-project.org/Licenses/
#





# ### add new branches:
# ### http://r-pkgs.had.co.nz/git.html#git-branch
# git checkout -b faster_01
# git push --set-upstream origin faster_01






#' @import dendextend
#' @import ggplot2
#' @import magrittr
#' @import RColorBrewer

# http://stackoverflow.com/questions/10325231/when-writing-my-own-r-package-i-cant-seem-to-get-other-packages-to-import-corr

#' @importFrom plotly plotly ggplotly plotly_empty subplot layout hide_colorbar config style add_trace
#' @importFrom scales col_factor col_numeric
#' @importFrom viridis viridis
#' @importFrom stats as.dendrogram dendrapply dist hclust is.leaf order.dendrogram reorder sd
#' @importFrom seriation seriate get_order
#' @importFrom dendextend set is.dendrogram is.hclust seriate_dendrogram rotate color_branches find_k as.ggdend
#' @importFrom stats ecdf na.omit as.dist cor
#' @importFrom htmlwidgets saveWidget
#' @importFrom plotly plot_ly add_segments
#' @importFrom assertthat assert_that
#' @importFrom grDevices dev.new
#' @importFrom assertthat assert_that

#'
NULL







#
#
#
#
#
#
#
#
# .onLoad <- function(libname, pkgname){
#    # Thanks for Romain: http://stackoverflow.com/questions/4369334/first-lib-idiom-in-r-packages
#
#    # adding and removing menus from the Rgui when loading and detaching the library
#    # setHook(packageEvent("installr", "attach"), {function(pkgname, libpath) {add.installr.GUI()}  } )
#    # setHook(packageEvent("heatmaply", "detach"), {function(pkgname, libpath) {remove_heatmaply_options()}  } )
#
#    # set default options for heatmaply
#    setHook(packageEvent("heatmaply", "onLoad"), {function(pkgname, libpath) {assign_heatmaply_options()}  } )
#
#    # Does NOT work!
#    # remove_heatmaply_options is currently an empty function. In the future, it should
#    # remove default options for heatmaply when unloading
#    setHook(packageEvent("heatmaply", "onUnload"), {function(pkgname, libpath) {remove_heatmaply_options()}  } )
#    setHook(packageEvent("heatmaply", "detach"), {function(pkgname, libpath) {remove_heatmaply_options()}  } )
#
#    # heatmaply::heatmaply_options()
#
#    # set default options for d3 dendrogram.
#    d3dendro_defaults(D3DENDRODEFAULTS)
# }
#
# # menus are added and removed as needed: !!
#

.onAttach <- function(lib, pkg, ...) {
  packageStartupMessage(heatmaplyWelcomeMessage())
}

#
#


heatmaplyWelcomeMessage <- function() {
  # library(utils)

  paste0(
    "\n",
    "======================\n",
    "Welcome to heatmaply version ", utils::packageDescription("heatmaply")$Version, "\n",
    # "\n",
    "\n",
    "Type citation('heatmaply') for how to cite the package.\n",
    "Type ?heatmaply for the main documentation.\n",
    "\n",
    "The github page is: https://github.com/talgalili/heatmaply/\n",
    "Please submit your suggestions and bug-reports at: https://github.com/talgalili/heatmaply/issues\n",
    "You may ask questions at stackoverflow, use the r and heatmaply tags: \n\t https://stackoverflow.com/questions/tagged/heatmaply\n",
    # "\n",
    # "\tTo suppress this message use:  ", "suppressPackageStartupMessages(library(heatmaply))\n",
    "======================\n"
  )
}




# using "zzz.r" like in devtools...

# When adding new files, make sure they are listed in DESCRIPTION:
# Collate:
#    'create.global.library.r'
# 'install.r'
# 'updateR.r'




# library(heatmaply)
# environmentIsLocked(as.environment("package:heatmaply"))
# lockEnvironment(env=as.environment("package:heatmaply"), bindings = FALSE)
# lockEnvironment(env=as.environment("package:heatmaply"), bindings = TRUE)


# IMPORTANT NOTICE: this will add Collate to the DESCRIPTION file, and if any new r file is added - it will need to be updated.
# Collate:
# +    'create.global.library.r'
# +    'install.r'
# +    'updateR.r'
# +    'zzz.r'


############
## OLD
# Steps:
# http://r.789695.n4.nabble.com/vignettes-problems-with-PDF-compaction-td4664909.html
# 1) install gs - http://www.ghostscript.com/download/gsdnld.html
# 2) find where it is, and update R_GSCMD:
# Sys.setenv(R_GSCMD="C:\\Program Files\\gs\\gs9.10\\bin\\gswin64c.exe")
# Sys.setenv(R_GSCMD="C:\\Program Files\\gs\\gs9.14\\bin\\gswin64c.exe")
# Sys.setenv(R_GSCMD="D:\\temp\\qpdf-5.1.2\\bin\\qpdf.exe")
# Sys.getenv("R_GSCMD")
# 3) Check that it works:
# system2(Sys.getenv("R_GSCMD"), args="--version")
# 4) use:
# library(tools)
# tools::compactPDF("inst\\doc\\heatmaply-tutorial.pdf", gs_quality="printer")
# tools::compactPDF("inst\\doc\\heatmaply-tutorial.pdf",
# qpdf = "D:\\temp\\qpdf-5.1.2\\bin\\qpdf.exe", gs_cmd = "C:\\Program Files\\gs\\gs9.14\\bin\\gswin64c.exe")
#### tools::compactPDF("inst\\doc\\heatmaply-tutorial.pdf", gs_quality="ebook")
#### tools::compactPDF("inst\\doc\\heatmaply-tutorial.pdf", gs_quality="screen")
#### tools::compactPDF("vignettes\\heatmaply-tutorial.pdf")
###   compacted 'heatmaply-tutorial.pdf' from 964Kb to 737Kb
#### tools::compactPDF("vignettes\\heatmaply-tutorial.pdf", gs_quality="ebook")

# For checking:
# 1) get qpdf
#     http://sourceforge.net/projects/qpdf/files/
# 2) put it somewhere
# 3) set R_QPDF
#  Sys.setenv(R_QPDF="C:\\Rtools\\qpdf-5.1.1\\bin\\qpdf.exe")
#  Sys.which(Sys.getenv("R_QPDF", "qpdf"))

# Also, make sure to add:
# options(repos=c("http://cran.rstudio.com", "http://www.stats.ox.ac.uk/pub/RWin" ))
# to D:\R\R-devel\etc\Rprofile.site

##############







##########
##########
##########
##########
## NEW
# How to deal with compression:
# 1) Download the latest qpdf: http://sourceforge.net/projects/qpdf/files/  (and place it somewhere)
# 2) Install gs - http://www.ghostscript.com/download/gsdnld.html
# 3) Run the following:

# tools::compactPDF("inst\\doc\\heatmaply-tutorial.pdf",
#                   qpdf = "C:\\Program Files (x86)\\qpdf-5.1.2\\bin\\qpdf.exe",
#                   gs_cmd = "C:\\Program Files\\gs\\gs9.14\\bin\\gswin64c.exe",
#                   gs_quality="ebook")

##########
##########
##########



# https://stat.ethz.ch/pipermail/r-help/2010-September/251194.html
# tools::showNonASCII( readLines("vignettes\\FAQ.Rmd"))
#





####### Cool stuff to add:
# library(devtools)
# use_code_of_conduct()
# use_cran_badge()
# use_coveralls()
# #



# install.packages("C:\\Dropbox\\aaaa good R code\\AA - My packages\\heatmaply_1.0.0.tar.gz", repos = NULL, type="source")

#
# # Run once:
# shell('set PATH=%PATH%;"C:\\Program%20Files%20(x86)\\Git\\bin"', intern = TRUE)
# shell("echo %PATH% ", intern= TRUE)
#
# system('set PATH=%PATH%;C:\\xampp\\php')
#
#
#
# # Creating a changelog using git
# First make sure git is in the path. Run the
# following using cmd.exe, as admin:
# setx PATH "C:\\Program Files (x86)\\Git\\bin"
#
# Then - run the script to create the ChangeLog before shipping the package.
# # http://stackoverflow.com/questions/10330425/how-do-i-export-a-git-log-to-a-text-file
# # http://stackoverflow.com/questions/3523534/good-ways-to-manage-a-changelog-using-git
# # http://www.commandlinefu.com/commands/view/12420/generate-a-change-log-with-git
# shell("git log --decorate > ChangeLog", intern = T)

# Modify it using: http://git-scm.com/book/en/Git-Basics-Viewing-the-Commit-History
#         http://stackoverflow.com/questions/9007181/custom-log-format-omits-newline-at-end-of-output
# shell('git log --graph --stat --date=iso > ChangeLog', intern = TRUE)
# use this:
# shell('git log --graph --stat --date=short --pretty=format:"%ad(%an) %s |%h" > ChangeLog', intern = TRUE)
#
# system.PATH()
# shell("path")


# shell("echo %PATH% ", intern= TRUE)
# library(rmarkdown)
# rmarkdown::render("NEWS",clean = TRUE,output_format = "html_document")



# https://github.com/r-lib/styler
# # install.packages("remotes")
# remotes::install_github("krlmlr/styler")
# styler::style_pkg()

# devtools::spell_check()




# Search [^\x00-\x7F]+
# with notepad++ with regex, in order to find non-ascii values.
# Source: http://stackoverflow.com/questions/20889996/notepad-how-to-remove-all-non-ascii-characters-with-regex




# when a function is renamed, its document in man must be removed - otherwise it may cause problems with the built check (it will try to run the code in the example, and will fail.)
# When all is done, run:
# library(devtools)
# check()
# browseURL(tempdir())
### http://www.rstudio.com/ide/docs/packages/build_options
#
# devtools::check(build_args="--no-build-vignettes --no-manual", args = "--no-examples --no-build-vignettes --no-manual",  cran = FALSE, cleanup = FALSE)
# check(build_args="--no-build-vignettes --no-manual", args = "--no-build-vignettes --no-manual",  cran = FALSE, cleanup = FALSE)
# check(build_args="--no-build-vignettes ", args = "--no-build-vignettes",  cran = FALSE, cleanup = FALSE)
# devtools::check(args="--as-cran")
# devtools::check("C:/Dropbox/aaaa good R code/AA - My packages/heatmaply", args="--as-cran")
#                 Thanks to: http://stackoverflow.com/questions/10017702/r-cmd-check-options-for-more-rigorous-testing-2-15-0


# shell('git log --graph --stat --date=short --pretty=format:"%ad(%an) %s |%h" > ChangeLog', intern = TRUE)
# system('git log --graph --stat --date=short --pretty=format:"%ad(%an) %s |%h" > ChangeLog', intern = TRUE)
# file.copy("NEWS", "NEWS.md",overwrite = TRUE)
# devtools::check_win_devel()
# pkgdown::build_home()
# pkgdown::build_site(run_dont_run = F)
# pkgdown::build_news()
# release()