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server.R
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server.R
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#
# This is the server logic of a Shiny web application. You can run the
# application by clicking 'Run App' above.
#
server <- function(input, output, session) {
# maximum uploaded file size limit
options(shiny.maxRequestSize=16000*1024^2)
#source(file.path("R", "DimPlotly.R"), local = TRUE)$value
# global variables
RV <- reactiveValues(mass_table = NULL,
user_formula = NULL,
user_formula_ionization = NULL,
user_formula_count_table = NULL,
user_formula_compound_mass = 0,
user_formula_compound_atom_diversity = 0,
user_formula_compound_n_atoms = 0,
user_brick_input_counter = 0,
user_brick_input_table = data.frame(Symbol = character(),
Count = numeric(),
Status = character(),
RelMass = numeric(),
stringsAsFactors = FALSE),
adduct_total_mass = NULL,
modifier_total_mass = NULL,
user_charge = -1,
formula_table = data.frame(MoleculeName = character(),
Formula = character()),
user_modfier_input_table = data.frame(Bricks = character(),
RelMass = numeric(),
Charge = numeric(),
stringsAsFactors = FALSE),
single_formula_adduct_table = data.frame(Formula = character(),
Mass = numeric(),
Modifier = character(),
RelMass = numeric(),
Charge = numeric(),
AdductMass = numeric(),
stringsAsFactors = FALSE),
multiple_formula_adduct_table = data.frame(MoleculeName = character(),
Formula = character(),
Mass = numeric(),
Modifier = character(),
RelMass = numeric(),
Charge = numeric(),
AdductMass = numeric(),
stringsAsFactors = FALSE),
mass_to_predict_formula_table = data.frame(ID = character(),
META = character(),
Mass = numeric()),
prediction_results_table = NULL,
mass_to_pool_table = NULL,
mass_to_pool_result = NULL,
sequence_table = NULL,
sample_block_size = 0,
sample_block_n = 0,
total_blank_n = 0,
blank_block_n = 0,
sequence_result_table = data.frame(SampleType = character(),
FileName = character(),
Path = character(),
InstrumentMethod = character(),
Position = numeric(),
InjVol = numeric(),
stringsAsFactors = FALSE),
sequence_trials = 0,
mgf_spectrum_count = 0,
mgf_ms1_count = 0,
mgf_ms2_count = 0,
mgf_data = list(),
selected_spectrum = NULL)
# TAB Load data
source(file.path("server", "tab1_load_mass_data.R"), local = TRUE)$value
# TAB Define modifier
source(file.path("server", "tab2_define_modifier.R"), local = TRUE)$value
# TAB Work formula
source(file.path("server", "tab3_work_formula.R"), local = TRUE)$value
# TAB Compute list of adducts
source(file.path("server", "tab4_compute_list_of_adducts.R"), local = TRUE)$value
# TAB Predict formula from mass
source(file.path("server", "tab5_predict_formula_from_mass.R"), local = TRUE)$value
# TAB Generate pools
source(file.path("server", "tab6_generate_mass_pools.R"), local = TRUE)$value
# TAB Build sequence
source(file.path("server", "tab7_build_sequence.R"), local = TRUE)$value
# TAB mgf reader
source(file.path("server", "tab8_mgf_reader.R"), local = TRUE)$value
############################################################################
# #
# Session information #
# #
############################################################################
output$session_information <- renderPrint({
print(sessioninfo::session_info())
})
############################################################################
# #
# Help messages #
#
# use : https://dillinger.io
#
############################################################################
observeEvent(input$tab1_load_mass_data_help, {
showModal(modalDialog(
title = "Tab 1 help",
renderUI(HTML(includeMarkdown("vignettes/tab1_load_mass_data_help.md"))),
easyClose = TRUE
))
})
observeEvent(input$tab2_define_modifier_help, {
showModal(modalDialog(
title = "Tab 2 help",
renderUI(HTML(includeMarkdown("vignettes/tab2_define_modifier_help.md"))),
easyClose = TRUE
))
})
observeEvent(input$tab3_work_formula_help, {
showModal(modalDialog(
title = "Tab 3 help",
renderUI(HTML(includeMarkdown("vignettes/tab3_work_formula_help.md"))),
easyClose = TRUE
))
})
observeEvent(input$tab4_compute_list_of_adducts_help, {
showModal(modalDialog(
title = "Tab 4 help",
renderUI(HTML(includeMarkdown("vignettes/tab4_compute_list_of_adducts_help.md"))),
easyClose = TRUE
))
})
observeEvent(input$tab5_predict_formula_from_mass_help, {
showModal(modalDialog(
title = "Tab 5 help",
renderUI(HTML(includeMarkdown("vignettes/tab5_predict_formula_from_mass_help.md"))),
easyClose = TRUE
))
})
observeEvent(input$tab6_generate_mass_pools_help, {
showModal(modalDialog(
title = "Tab 6 help",
renderUI(HTML(includeMarkdown("vignettes/tab6_generate_mass_pools_help.md"))),
easyClose = TRUE
))
})
observeEvent(input$tab7_build_sequence_help, {
showModal(modalDialog(
title = "Tab 7 help",
renderUI(HTML(includeMarkdown("vignettes/tab7_build_sequence_help.md"))),
easyClose = TRUE
))
})
observeEvent(input$tab8_mgf_reader_help, {
showModal(modalDialog(
title = "Tab 8 help",
renderUI(HTML(includeMarkdown("vignettes/tab8_mgf_reader_help.md"))),
easyClose = TRUE
))
})
}