global.R

enableBookmarking(store = 'server')

library(shiny)
library(ftmsRanalysis)
library(ggplot2)
library(reshape2)
library(webshot)
library(htmlwidgets)
library(dplyr)
library(markdown)
library(raster)
library(purrr)
library(shinyBS)
library(shinyjs)
library(shinyWidgets)
library(pander)
library(readr)
library(plotly)
library(DT)
library(shinycssloaders)
library(mapDataAccess)
library(shinybusy)

# uncomment either library() or load_all() if you need to load kegg
library(KeggData)
library(MetaCycData)
# devtools::load_all('~/Documents/git_repos/MetaCycData/')
# devtools::load_all('~/Documents/git_repos/KeggData/')

# static variables #
dt_checkmark <- '<span class="glyphicon glyphicon-ok" style="color:deepskyblue"></span>'
dt_minus <- '<span class="glyphicon glyphicon-minus"></span>'

element_ratios_info <- 'Comma-seperated list of ratios of any present pair of elements. Examples: "O:C, N:P,"H:C".'
dbe_opts_info <- 'Semicolon separated strings of elements and their valences, i.e. to calculate the dbe for two sets of valences, input C4H1N3O2S2P3;C3H3N2O2S4P4'
kendrick_opts_info <- 'The base compound(s) used to calculate the Kendrick Mass.  See <a href = ""https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5447562/"">[Foquet and Sato, 2017]</a> for details.'

dt_checkmark <- '<span class="glyphicon glyphicon-ok" style="color:deepskyblue"></span>'
dt_minus <- '<span class="glyphicon glyphicon-minus"></span>'

ttip_text = list("plot_save" = "Save the last created plot", "plot_review" = "Review saved plots", "page_help" = "How do I use this page?")

#------ Download Example Data ---------#
example_edata <- read_csv('Data/example12T_edata.csv') %>% as.data.frame(stringsAsFactors = FALSE)
example_emeta <- read_csv('Data/example12T_emeta.csv') %>% as.data.frame(stringsAsFactors = FALSE)
calc_opts <- read_csv('calculation_options.csv') %>% as.data.frame(stringsAsFactors = FALSE)
calc_vars <- read_csv('calculation_variables.csv') %>% as.data.frame(stringsAsFactors = FALSE)
# determines when 'large data' options are triggered
max_cells <- 2000000

info_text = list(
  COREMS_UPLOAD_ERROR = "There was an error retrieving your Core-MS files: %s",
  COREMS_UPLOAD_NOSAMPS = "No files found in the cloud location specified by 'corems-prefix' in the URL.",
  COREMS_UPLOAD_SUCCESS = "The following files were uploaded from Core-MS: <br>",
  VALID_LINKED_PLOTS = "Current valid plots to link are Van-Krevelen, Kendrick, single sample density, and custom scatter plots."
)

# cloud/minio resources
VALID_MINIO_HEADER_PARAMS = c("corems-prefix", "map-object")

#' @SECTION Variables for selectors/inputs ##

# Use this global variable for 'nothing selected' options
NULLSELECT__ = "__nullselect__"

# list of arguments to be passed to as.CoreMSData that need an input picker
COREMSDATA_ARGS = c(
  "index_cname",
  "obs_mass_cname",
  "calc_mass_cname",
  "calib_mass_cname",
  "pheight_cname",
  "error_cname",
  "conf_cname",
  "heteroatom_cname",
  "iontype_cname",
  "file_cname",
  "monoiso_index_cname",
  "mf_cname",
  "c13_cname",
  "o18_cname",
  "n15cname",
  "s34_cname"
)

COREMSDATA_OPTIONAL_ARGS = c("c13_cname", "o18_cname", "n15cname", "s34_cname")
COREMSDATA_REQ_ARGS = setdiff(COREMSDATA_ARGS, COREMSDATA_OPTIONAL_ARGS)

# Isotopes as determined by CoreMS static files
COREMS_ISOTOPES = jsonlite::read_json("isotopes.json")
COREMSDATA_ISOTOPE_ARGS = list("c13_cname" = "13C", "o18_cname" = "18O", "n15cname" = "15N", "s34_cname" = "34S")

FREDA_ISOTOPES_OF_INTEREST = c("34S", "18O", "13C", "15N")