inst/shinyapp/app.R
In BIMIB-DISCo/LACE: Longitudinal Analysis of Cancer Evolution (LACE)
### app.R --
###
### Main LACEinterface file.
###
### See file LICENSE in the main folder for licensing and copyright
### information.
### reactlogShow(time = FALSE)
### Libraries needed by the app.
suppressMessages(library(biomaRt, exclude = c("show", "select")))
suppressMessages(library(foreach))
suppressMessages(library(doParallel))
suppressMessages(library(sortable))
suppressMessages(library(shiny,
exclude = c("runExample",
"dataTableOutput",
"renderDataTable",
"validate",
"show")))
suppressMessages(library(shinythemes))
suppressMessages(library(dplyr))
suppressMessages(library(forcats))
suppressMessages(library(tidyr))
suppressMessages(library(readr))
suppressMessages(library(shinyFiles))
suppressMessages(library(shinyjs, exclude = c("show")))
## library(shinyBS)
suppressMessages(library(jsonlite))
suppressMessages(library(configr))
## library(readr)
suppressMessages(library(DT))
suppressMessages(library(stringr))
suppressMessages(library(tools))
suppressMessages(library(fs))
suppressMessages(library(data.table, exclude = c("first", "last", "between")))
suppressMessages(library(htmltools))
suppressMessages(library(shinyBS))
suppressMessages(library(bsplus))
suppressMessages(library(shinydashboard))
suppressMessages(library(shinyvalidate))
suppressMessages(library(logr))
suppressMessages(library(ggplot2))
suppressMessages(library(svglite))
#library(widgetframe)
### Code
### ====
### getWidgetType --
getWidgetType <- function(widgetId) {
paste0("elem = document.getElementById('", widgetId, "');
var message;
if (elem == null) {
message = 'None'
} else {
// RStudio Viewer + IE workaround (dont have .include())
if (elem.getAttribute('class').indexOf('js-range-slider') > -1) {
message = 'slider'
} else if (elem.getAttribute('class').indexOf('shinyFiles') > -1) {
message = 'shinyFiles'
} else if (elem.getAttribute('class').indexOf('shinyDirectories') > -1) {
message = 'shinyDirectories'
} else if (elem.nodeName == 'SELECT') {
message = 'select'
} else if (elem.getAttribute('class').indexOf('shiny-text-output') > -1) {
message = 'shiny-text-output'
} else if (elem.getAttribute('class').indexOf('selectized') > -1) {
message = 'selectized'
} else {
message = elem.getAttribute('type');
}
}
Shiny.onInputChange('inputType_", widgetId,"', message)
"
)
}
### jsCode --
jsCode <- "shinyBS.addTooltip = function(id, type, opts) {
var $id = shinyBS.getTooltipTarget(id);
var dopts = {html: true};
opts = $.extend(opts, dopts);
if (type == 'tooltip') {
$id.tooltip('destroy');
setTimeout(function() { $id.tooltip(opts); }, 200);
} else if(type == 'popover') {
$id.popover('destroy');
setTimeout(function() { $id.popover(opts); }, 200);
}
}"
log2_print <- function(x, msg = "") {
if (str_length(msg)>0)
log_print(msg, console = FALSE, blank_after = FALSE, hide_notes =TRUE)
log_print(x, console = FALSE, blank_after = FALSE, hide_notes =FALSE)
}
#log2_print <- function(x, msg = "") {}
### compare_named_lists --
###
### Notes:
### MA: Seems a bit complicated. What is this supposed to do?
compare_named_lists <- function(l1, l2) {
if (is.list(l1) && is.list(l2)) { # if they are lists
if (length(unique(names(l1))) == length(l1) &&
length(unique(names(l2))) == length(l2) &&
!("" %in% names(l1)) &&
!("" %in% names(l2))
) { # if they are named
st <- TRUE
for (i in unique(c(names(l1), names(l2)))) {
## If the same name is present in both..
##
## Notes:
## MA: are we sure there is no 'intersection' operation on
## lists in R?
if (i %in% names(l1) && i %in% names(l2)) {
if (is.list(l1[[i]]))
st <- st && compare_named_lists(l1[[i]], l2[[i]])
else
st <- st && identical(l1[[i]], l2[[i]])
}
else
return(FALSE)
}
return(st)
}
return(FALSE)
}
else
return(FALSE)
}
### Help Management
### ===============
source("info_help.R")
### make_shiny_help_popover --
make_shiny_help_popover <- function(for_object,
pop_title,
pop_text,
with_icon = shiny_iconlink(),
server = FALSE) {
with_icon <- with_icon %>%
bs_embed_popover(title = pop_title,
content = pop_text,
placement = "right",
trigger = "hover",
delay = list("show" = 200, "hide" = 3000),
html = TRUE
)
for_object <- for_object %>% shinyInput_label_embed(with_icon)
if (server)
for_object <-
tagList(for_object,
tags$script("$(function () {$('[data-toggle=\"popover\"]').popover()})")
)
return(for_object)
}
### make_title_help_popover
make_title_help_popover <- function(for_object,
near_label,
pop_title,
pop_text,
with_icon = shiny_iconlink(),
server = FALSE) {
with_icon <- with_icon %>%
bs_embed_popover(title = pop_title,
content = pop_text,
placement = "right",
trigger = "hover",
delay= list("show"= 200, "hide"= 3000),
html = TRUE
)
with_icon <- htmltools::div(class = "pull-right", with_icon)
tag <- htmltools::div(class = "form-group shiny-input-container",
near_label,
br(),
for_object)
tag$children[[1]] <-
tag$children[[1]] %>%
htmltools::tagAppendChild(with_icon) %>%
htmltools::tagAppendAttributes(style = "width:100%;")
if (server)
tag <-
tagList(tag,
tags$script("$(function () {$('[data-toggle=\"popover\"]').popover()})")
)
return(tag)
}
### inline --
inline = function (x) {
tags$div(style="display:inline-block;", x)
}
### ui -- ####
ui <- fluidPage(
## singleton(tags$head(tags$script(src = "bs.js"))),
useShinyjs(),
withMathJax(),
## extendShinyjs(text = jsCode, functions = c("addTooltip")),
## extendShinyjs(text = jsCode, functions = c("bsPopover")),
tags$head(tags$style("@import url(https://use.fontawesome.com/releases/v5.7.2/css/all.css);"),
tags$style(HTML(".bucket-list-container {min-height: 290px; max-height: 300px;}")),
tags$style(HTML(".rank-list {min-height: 100px; max-height: 240px; overflow-y: scroll;}")),
#tags$style(HTML(".shinyDirectories, .shinyFiles { width: 100%; direction: rtl; white-space: nowrap; overflow: hidden; text-overflow: ellipsis;}")),
tags$style(HTML(".shinyDirectories, .shinyFiles { width: 100%; white-space: nowrap; overflow: hidden; text-overflow: ellipsis;}")),
tags$style(type="text/css", "body {padding-bottom: 70px;}"),
tags$style(HTML(".content-wrapper, .right-side {background-color: #ffffff;}"))
),
use_bs_popover(),
dashboardPage(
dashboardHeader(
title = "LACE 2.0",
tags$li(class = "dropdown",
tags$a(uiOutput("pr_title_ui_h")
)
)
),
dashboardSidebar(
sidebarMenu( id = "sidemenu",
hidden(menuItem("hidden_menu31", tabName = "hidden_menu31")),
menuItem(
"Application",
tabName = "application",
icon = icon("braille"), #icon("window-maximize"),
hidden(menuItem("hidden_menu3", tabName = "hidden_menu3")),
menuSubItem("New Project", tabName = "new_proj", icon = icon("layer-group") ),
menuSubItem("Quit", tabName = "quit_app", icon = icon("power-off") )#,
#actionButton("quit_app", "Quit")
),
hidden(menuItem("hidden_menu", tabName = "hidden_menu")),
menuItem(
"Projects",
tabName = "Projects",
icon = icon("cubes"),
#expandedName = "ttt",
menuItemOutput("recent_projects"),
hidden(menuItem("hidden_menu2", tabName = "hidden_menu2")),
# menuItem(
# "Recent Projects",
# tabName = "Recent Projects",
# icon = icon("th"),
# #expandedName = "projects",
# menuSubItem(
# "test22",
# tabName = ",media,disco,work_folder,Downloads,gitlace,LACEinterface,test2",
# #icon = icon("th"),
# #inline(actionButton("save_tab", "save")),
# #inline(actionButton("load_tab", "load"))
# ),
# menuSubItem(
# "test2",
# tabName = ",media,disco,work_folder,Downloads,gitlace,LACEinterface,test2",
# #icon = icon("th"),
# #inline(actionButton("save_tab", "save")),
# #inline(actionButton("load_tab", "load"))
# )#,
# #hidden(menuItem("hidden_menu4", tabName = "hidden_menu4"))
# ),
menuItem(
"Demo Projects",
tabName = "Demo Projects",
icon = icon("database"),
#expandedName = "demos",
menuSubItem(
"Melanoma dataset (Rambow)",
tabName = "Melanoma dataset",
#icon = icon("th"),
#inline(actionButton("save_tab", "save")),
#inline(actionButton("load_tab", "load"))
),
menuSubItem(
"Small dataset",
tabName = "Small dataset",
#icon = icon("th")#,
#inline(actionButton("save_tab", "save")),
#inline(actionButton("load_tab", "load"))
)#,
#hidden(menuItem("hidden_menu3", tabName = "hidden_menu3"))
)#,
#hidden(menuItem("hidden_menu1", tabName = "hidden_menu1"))
),
menuItem(
"Current Project",
tabName = "dashboard",
icon = icon("cube"),
hidden(menuItem("hidden_menu2", tabName = "hidden_menu2")),
#menuSubItem("Close Project", tabName = "close_proj", icon = icon("times-circle") ),
#actionButton("close_proj", "Close Project"),
menuItem(
"Save and Load Current Tab",
tabName = "dashboard_save",
icon = icon("th"),
hidden(menuItem("hidden_menu_SLpre", tabName = "hidden_menu_SLpre")),
menuSubItem("Save", tabName = "save_tab", icon = icon("download") ),
menuSubItem("Load", tabName = "load_tab", icon = icon("upload") ),
menuSubItem("Reset project", tabName = "load_tabs"),
hidden(menuSubItem("hidden_menu_SL", tabName = "hidden_menu_SL"))
#inline(actionButton("save_tab", "Save")),
#inline(actionButton("load_tab", "Load"))
)
)#,
#,
# menuItem(
# "Save and Load All Tabs",
# tabName = "dashboard",
# icon = icon("th"),
# inline(actionButton("save_tab", "save")),
# inline(actionButton("load_tab", "load"))
# ),
# menuItem(
# "Reset Tabs",
# tabName = "dashboard",
# icon = icon("th"),
# inline(actionButton("save_tab", "Clean and restore "))
# )
),
collapsed = FALSE
),
dashboardBody(
tabItems(
tabItem(tabName = "hidden_menu"),
tabItem(tabName = "Small dataset"),
tabItem(tabName = "Melanoma dataset"),
tabItem(tabName = "test22"),
tabItem(tabName = "test2")
),
div(id = "computation_idCol_div",
h3("Processing ... please wait")
),
fluidRow(
column(width = 12,
tabsetPanel(id = "main_tabset",
type = "tabs",
## Project tab
tabPanel(
"Project",
br(),
uiOutput("pr_title_ui"),
br(),
helpText(text[["pr_tab_help"]]),
br(),br(),
shinyDirButton('pr_folder',
'Select folder',
'Please select the project root folder', FALSE) %>%
make_title_help_popover (
tags$b("Project root folder"),
"Project folder",
text[["pr_folder"]]
),
br(),
textInput("pr_name",
"Name",
placeholder = "Your project name") %>%
make_shiny_help_popover(
"Project name",
text[["pr_name"]]
),
br(),br(),
div(id = "pr_path_div",
uiOutput("pr_path_ui")
),
actionButton("pr_next", "Create project"),
br(),br(),
),
## Metadata tab
tabPanel(
"SC metadata",
br(),
tags$h3("Single cell metadata info"),
br(),
helpText(text[["m_tab_help"]]),
br(), br(),
shinyFilesButton('sc_metadata_file',
'Select file',
'Please select the experiment metadata file', FALSE) %>%
make_title_help_popover (
tags$b("Metadata file"),
"Metadata info file",
text[["sc_metadata_file"]],
server = TRUE
),
br(),
br(),
div(id = "m_idCol_div",
uiOutput("m_idCol")
),
tableOutput("m_id_column_tab"),
br(),
div(id="m_timePointsCol_div",
uiOutput("m_timePointsCol")
),
div(id="m_timePoints_div",
uiOutput("m_timePoints")
),
br(), br(),
),
## Annotation tab
tabPanel(
"Annotations",
br(),
tags$h3("Gene variant annotations"),
br(),
helpText(text[["av_tab_help"]]),
br(), br(),
## runjs(jsCode),
shinyDirButton('av_anovar_exec_dir',
'Select folder',
'Please select Annovar executable folder',
FALSE) %>%
make_title_help_popover (
tags$b("Annovar executable folder"),
"Annovar",
text[["av_anovar_exec_dir"]]
),
br(),
br(),
shinyDirButton('av_anovar_db_dir',
'Select folder',
'Please select Annovar reference database folder',
FALSE) %>%
make_title_help_popover (
tags$b("Annovar reference database"),
"Annovar reference database",
text[["av_anovar_db_dir"]]
),
br(),
br(),
shinyDirButton('av_vcf_in_dir',
'Select folder',
'Please select VCF folder',
FALSE) %>%
make_title_help_popover (
tags$b("Variant calling files folder"),
"Variant calling files folder",
text[["av_vcf_in_dir"]]
),
br(),
br(),
## tags$b("Output folder"),
## br(),
## shinyDirButton('av_out_dir', 'Select folder', 'Please select output folder', FALSE),
br(),
br(),
tags$b("Run"),
br(),
actionButton("av_exec",
"Annotate variants"),
# tags$span(icon("info-circle"),
# id = "icon_av_exec",
# style = "color: blue;"),
# bsPopover("icon_av_exec",
# "Load inputs",
# text[["av_exec"]],
# placement = "right",
# trigger = "hover",
# options = list("delay': {show : 500, hide : 2000}, 'a" = "show")),
br(),br(),
## tags$b("Result"),
## br(),
## verbatimTextOutput("av_anovar_exec_dir"),
## verbatimTextOutput("av_anovar_db_dir"),
## verbatimTextOutput("av_vcf_out_dir")
),
## Filters tab
tabPanel(
"Filters",
br(),
tags$h3("Quality filters"),
br(),
helpText(text[["thr_tab_help"]]),
br(), br(),
numericInput(
inputId = "thr_alleles_ratio",
label = "Alternate frequency",
min = 1,
max = 500,
step = 1,
value = 2
) %>%
make_shiny_help_popover(
"Cell alternate allele frequency",
text[["thr_alleles_ratio"]]
),
numericInput(
inputId = "thr_maf",
label = "MAF",
min = 0.01,
max = 0.5,
step = 0.005,
value = 0.01
) %>%
make_shiny_help_popover(
"Minor alleles frequency",
text[["thr_maf"]]
),
numericInput(
inputId = "thr_freq",
label = "Variant frequency",
min = 0.,
max = 1,
step = 0.01,
value = 0.01
) %>%
make_shiny_help_popover(
"Sample variant frequency",
text[["thr_freq"]]
),
br(),
div(id = "thr_bucket_var_list_div",
uiOutput("thr_bucket_var_list")
),
br(),br(),br(),br(),
tags$b("Run"),
br(),
actionButton("thr_exec", "Apply filters"),
br(),br(),
## tags$b("Result"),
## verbatimTextOutput("thr_filters"),
## verbatimTextOutput('thr_accepted_var'),
## verbatimTextOutput('thr_negleted_var')
),
## Depth tab
tabPanel(
"SC sampling depths",
br(),
tags$h3("Single cell sampling depth"),
br(),
helpText(text[["dp_tab_help"]]),
br(), br(),
shinyDirButton('dp_samtools_exec_dir',
'Select folder',
'Please select samtools executable folder',
FALSE) %>%
make_title_help_popover (
tags$b("Samtools executable folder"),
"Samtools executable folder",
text[["dp_samtools_exec_dir"]]
),
br(), br(),
shinyDirButton('dp_bam_dir',
'Select folder',
'Please select folder containing the single cell BAM files',
FALSE) %>%
make_title_help_popover (
tags$b("BAMs folder"),
"BAMs folder",
text[["dp_bam_dir"]]
),
br(), br(),
tags$b("Output folder"),
br(), br(),
tags$b("Run"),
br(),
actionButton("dp_exec", "Compute depth"),
br(), br(),
## tags$b("Result"),
## br(),
## verbatimTextOutput("dp_par"),
),
## Variants tab
tabPanel(
"Variants",
br(),
tags$h3("Variant filters"),
br(),
helpText(text[["va_tab_help"]]),
fluidRow(column(4,
br(), br(),
numericInput(
inputId = "va_depth_minimum",
label = "Minimum depth",
min = 0,
max = 500,
step = 1,
value = 3
) %>%
make_shiny_help_popover(
"Minimum depth",
text[["va_depth_minimum"]]
),
br(),
numericInput(
inputId = "va_missing_values_max",
label = "Max missing value",
min = 0.0,
max = 1.0,
step = 0.05,
value = 0.4
) %>%
make_shiny_help_popover(
"Maximumax missing value",
text[["va_missing_values_max"]]
),
br(),
numericInput(
inputId = "va_minumum_median_total", # minimum median depth for total reads
label = "Site minumum median depth:",
min = 0,
max = 500,
step = 1,
value = 8
) %>%
make_shiny_help_popover(
"Minumum median depth per site",
text[["va_minumum_median_total"]]
),
br(),
numericInput(
inputId = "va_minumum_median_mutation", # minimum median depth for reads supporting mutations
label = "Mutation minimum median depth",
min = 0,
max = 500,
step = 1,
value = 4
) %>%
make_shiny_help_popover(
"Minimum median depth per mutation",
text[["va_minumum_median_mutation"]]
),
br(),
br(),
br(),
selectizeInput(
'va_verified_genes',
'Select variant genes',
NULL,
multiple = TRUE,
options = list (
placeholder = 'Choose genes for inferential analysis',
hideSelected = FALSE,
plugins =
list("drag_drop",
"remove_button",
"dropdown_header",
"restore_on_backspace"),
dropdown_header =
list(title = 'a')
)
) %>%
make_shiny_help_popover(
"Variant gene selection",
text[["va_verified_genes"]]
),
),
column(8,
br(),
br(),
#plot
plotOutput('va_filtered_bin_hmap', height = 600)
)
),
br(),
br(),
tags$b("Overview of post-filtered mutations"),
br(),
br(),
DTOutput("va_out"),
br(), br(),
tags$b("Run"),
br(),
actionButton("va_exec", "Select variants"),
br(),
br(),
## tags$b("Result"),
## verbatimTextOutput("va_filters")
),
## Inference tab
tabPanel(
"Inference",
br(),
tags$h3("Longitudinal tree inference parameters"),
br(),
helpText(text[["inf_tab_help"]]),
br(), br(),
numericInput(
inputId = "inf_learning_rate",
label = "Learning rate",
min = 0.01,
max = 10,
step = 0.1,
value = 1
) %>%
make_shiny_help_popover(
"Learning rate",
text[["inf_learning_rate"]]
),
br(),
div(id = "inf_alpha_div",
tagList(
br(),
span() %>%
make_title_help_popover (
tags$b("False positive rates"),
"False positive rate",
text[["inf_alpha"]]
),
span("Insert a set of false positive rates, one \\(\\alpha\\) for each sampling time point. Fill the last row to add further sets of rates to be used in the inference."),
DTOutput('inf_alpha', width = '100%'),
br()
)
),
## br(),
div(id = "inf_beta_div",
tagList(
br(),
span() %>%
make_title_help_popover (
tags$b("False negative rates"),
"False negative rate",
text[["inf_beta"]]
),
span("Insert a set of false negative rates, one \\(\\beta\\) for each sampling time point. Fill the last row to add further sets of rates to be used in the inference."),
DTOutput('inf_beta', width = '100%'),
br()
)
),
br(), br(),
numericInput(
inputId = "inf_num_iter",
label = "Number of iterations",
min = 100,
max = 4000,
step = 100,
value = 10000
) %>%
make_shiny_help_popover(
"Number of iterations",
text[["inf_num_iter"]]
),
br(),
numericInput(
inputId = "inf_num_rs",
label = "Number of restarts",
min = 1,
max = 100,
step = 10,
value = 50
) %>%
make_shiny_help_popover(
"Number of restarts",
text[["inf_num_rs"]]
),
br(),
numericInput(
inputId = "inf_n_try_bs",
label = "Early stopping",
min = 100,
max = 1000,
step = 100,
value = 500
) %>%
make_shiny_help_popover(
"Early stopping",
text[["inf_n_try_bs"]]
),
br(),
numericInput(
inputId = "inf_num_processes",
label = "Number of parallel processes",
min = 1,
max = 100,
step = 5,
value = 10
) %>%
make_shiny_help_popover(
"Number of parallel processes",
text[["inf_num_processes"]]
),
br(),
numericInput(
inputId = "inf_seed",
label = "Seed",
min = 0,
max = NA,
step = 1000,
value = 1121
) %>%
make_shiny_help_popover(
"Seed",
text[["inf_seed"]]
),
br(),
checkboxInput("inf_random_tree",
tags$b("Random tree intialization"),
FALSE) %>%
make_shiny_help_popover(
"Random tree intialization",
text[["inf_random_tree"]]
),
checkboxInput("inf_marginalize",
tags$b("Marginalize"),
FALSE) %>%
make_shiny_help_popover(
"Marginalize",
text[["inf_marginalize"]]
),
checkboxInput("inf_keep_equivalent",
tags$b("Keep equivalent"),
FALSE) %>%
make_shiny_help_popover(
"Keep equivalent",
text[["inf_keep_equivalent"]]
),
checkboxInput("inf_check_indistinguishable",
tags$b("Check indistinguishable"),
FALSE) %>%
make_shiny_help_popover(
"Check indistinguishable",
text[["inf_check_indistinguishable"]]
),
checkboxInput("inf_error_move",
tags$b("Error move"),
FALSE) %>%
make_shiny_help_popover(
"Error move",
text[["inf_error_move"]]
),
checkboxInput("inf_show",
tags$b("Show results in interface")) %>%
make_shiny_help_popover(
"Show results in interface",
text[["inf_show"]]
),
br(), br(),br(),
tags$b("Run"),
br(),
actionButton("inf_next", "Run LACE"),
br(), br(),
tags$b("Result"),
verbatimTextOutput("inf_par")
),
## results ####
tabPanel(
"Longitudinal display",
br(),
inline(actionLink("res_refresh", "Refresh page")),
inline(textOutput("res_lastrefresh")),
br(),
# #widgetframeOutput('LCT_FP', width = "1000px", height = "800px"),
# #LACE:::LACEOutput('LCT_FP'),#, width = 910, height = 800),
# {
# #x <-LACE:::LACEOutput('LCT_FP')
# #htmlwidgets::saveWidget(x,"LACE_result.html")
# NULL
# #x
# },
uiOutput("res"),
br(),br(),
)
)
)
)
)
)
)
### server -- ####
server <- function(input, output, session) {
setwd(.my_pkg_dir) # per non disperdersi
inputs <- list()
inputs[["null_reactiveVal"]] <- reactiveVal("")
observe({
input$null_reactiveVal > 0
}, )
types_ <- reactiveVal()
session$onSessionEnded(function() {
stopApp()
})
## Source?
source("check_demo.R", local = TRUE)
source("load_and_save.R", local = TRUE)
source("project_mgr.R", local = TRUE)
source("pipeline_io_ctrl.R")
source('alpha_beta_table.R', local = TRUE)
source("annotation.R")
source("filters_computation.R", local = TRUE)
source("depth_computation.R", local = TRUE)
source("step3_explore_lace_input_data.R")
source("make_lace_final_input.R")
default_yaml <-
list(".config_06_inf.yml" = list(),
".config_05_va.yml" = list(),
".config_04_dp.yml" = list(),
".config_03_thr.yml" = list(),
".config_02_av.yml" = list(),
".config_01_m.yml" = list()
)
os_hidden <- "."
os_conf <- list()
os_conf[["windows"]] <- "AppData"
os_conf[["mac"]] <- "Library"
os_conf[["unix"]] <- ".config"
os_conf_subdir = "config"
config_path = os_conf_subdir # to remove
## roots_dir=c(root = file.path('..'), "working_dir" = file.path('.'), getVolumes()())
roots_dir = c("project dir" = file.path("."),
".." = file.path(".."),
"../.." = file.path("..",".."),
"../../.." = file.path("..","..",".."),
getVolumes()())
## runjs(jsCode)
## runjs("console.log(shinyBS.addTooltip)")
## js$addTooltip("av_anovar_db_dir", "IL BOTTONE", "")
## addPopover(session, "av_anovar_db_dir", "IL BOTTONE2", "e il polpettone", placement = "right")
observe({
#browser()
if (!is.null(input$close)) {
if (input$close > 0) stopApp() # stop shiny
}
}, )
m_loaded_input_ <- reactiveVal()
av_loaded_input_ <- reactiveVal()
thr_loaded_input_ <- reactiveVal()
dp_loaded_input_ <- reactiveVal()
va_loaded_input_ <- reactiveVal()
inf_loaded_input_ <- reactiveVal()
rs_ <- reactiveVal()
inputs[["res_lastrefresh"]] <- reactiveVal("")
stime <- reactiveVal(2)
port <- reactiveVal()
sopt <- reactiveVal(callr::r_session_options())
av_grep_str= "^av_|^`av_|_av_"
thr_grep_str= "^thr_|^`thr_|_thr_"
dp_grep_str= "^dp_|^`dp_|_dp_"
va_grep_str= "^va_|^`va_|_va_"
inf_grep_str= "^inf_|^`inf_|_inf_"
m_grep_str= "^m_|^`m_|_m_|sc"
inf_uis = c("inf_num_iter",
"inf_num_rs",
"inf_n_try_bs",
"inf_num_processes",
"inf_seed",
"inf_random_tree",
"inf_marginalize",
"inf_keep_equivalent",
"inf_check_indistinguishable",
"inf_show",
"inf_learning_rate",
"inf_error_move")
va_uis= c('va_depth_minimum',
'va_missing_values_max',
'va_minumum_median_total',
'va_minumum_median_mutation')
thr_uis = c('thr_alleles_ratio',
'thr_maf',
'thr_freq',
'thr_accepted_var',
'thr_negleted_var')
dp_uis= c('dp_samtools_exec_dir', 'dp_bam_dir')
av_dir_uis = c('av_anovar_exec_dir',
'av_anovar_db_dir',
'av_vcf_in_dir')
source("project_tab.R", local = TRUE)
source("inference_tab.R", local = TRUE)
setwd(.my_actual_wd)
### Dashboard reactiveVals ####
inputs[["demo"]] <- reactiveVal()
inputs[["reload_project"]] <- reactiveVal()
inputs[["demo_remainder"]] <- reactiveVal()
inputs[["long_job"]] <- reactiveVal(0)
### End dashboard reactiveVals ####
### Dashboard observers ####
shinyjs::hide(id="computation_idCol_div")
observeEvent(inputs[["reload_project"]](), {
proj_dir <- inputs[["reload_project"]]()
if (inputs[["reload_project"]]() != 1 && inputs[["reload_project"]]() != 0)
{
if (dir.exists(proj_dir)) {
#browser()
hide_tab()
inputs[["reload_project"]](1)
inputs[["pr_path"]](proj_dir)
}
else
inputs[["reload_project"]](NULL)
}
#else
# inputs[["reload_project"]](NULL)
})
observeEvent( inputs[["demo"]](),{
if(inputs[["demo"]]() == "Small_dataset" || inputs[["demo"]]() == "Rambow_dataset")
{
#browser()
if(!check_demo()) {
inputs[["demo"]](NULL)
toggle_inputs(is.null(inputs[["demo"]]()))
showNotification("Impossible to download demos.", duration = 10, type = "warning")
}
else
{
#browser()
demo_dir<-file.path(.my_pkg_dir,inputs[["demo"]]())
# create tmp folder
tmp_dir <- tempdir()
tmp_path <- file.path(tmp_dir,inputs[["demo"]]())
dir.create(tmp_path, showWarnings = FALSE)
inputs[["demo_remainder"]](tmp_path)
# fill tmp folder
if (dir.exists(tmp_path) && dir.exists(demo_dir))
{
#delay(100, {
#browser()
hide_tab()
#})
dir_copy(demo_dir, tmp_path, overwrite = TRUE)
inputs[["demo"]](1) # temporary project ready
inputs[["pr_path"]](tmp_path)
}
else
{
#browser()
inputs[["demo"]](NULL)
toggle_inputs(is.null(inputs[["demo"]]()))
}
# disable tab
#shinyjs::addClass()
#shinyjs::disable(selector = '.nav-tabs a[data-value="SC metadata"')
#shinyjs::disable(selector = '.navbar-nav a[data-value="Annotations"')
# load output
}
}
#else
# inputs[["demo"]](NULL)
}, ignoreInit = TRUE)
# observeEvent(input[["sidebarItemExpanded"]], {
# print(input[["sidebarItemExpanded"]])
#
# if(input$sidebarItemExpanded == "projects") {
#
# }
# })
createmenuitem <- function(x, projs) {
#browser()
if (dir.exists(projs[[x]]))
menuSubItem(
text = names(projs)[x],
tabName = str_replace_all(
normalizePath(projs[[x]]),
pattern = .Platform$file.sep,
replacement = ","
)
)
else
NULL
}
observeEvent(input[["sidemenu"]], {
#browser()
projs <- update_proj_list(NULL)
# createmenuitem <- function(x) {
# menuSubItem(
# text = names(projs)[x],
# tabName = str_replace_all(
# normalizePath(projs[[x]]),
# pattern = .Platform$file.sep,
# replacement = ","
# )
# )
# }
submenus <- lapply(seq_along(projs), FUN = function(x) {createmenuitem(x,projs)})
recent_projects <- menuItem("Recent Projects", submenus,
icon = icon("history"))
output$recent_projects <- renderMenu({recent_projects})
log2_print(recent_projects, msg = "LACEview: recent projects =")
}, once = TRUE )
observeEvent( input[["sidemenu"]],{
log2_print(input[["sidemenu"]], msg = "LACEview:")
#browser()
if (input[["sidemenu"]] == "Small dataset") {
inputs[["demo"]]("Small_dataset")
}
if (input[["sidemenu"]] == "Melanoma dataset") {
inputs[["demo"]]("Rambow_dataset")
}
if (input[["sidemenu"]] != "Small dataset" && input[["sidemenu"]] != "Melanoma dataset") {
proj_dir <- str_replace_all(input[["sidemenu"]], pattern = ",", replacement = .Platform$file.sep)
inputs[["reload_project"]](proj_dir)
}
if (input[["sidemenu"]] == "save_tab")
save_tab()
if (input[["sidemenu"]] == "load_tab")
load_tab()
if (input[["sidemenu"]] == "load_tabs")
load_tabs()
if (input[["sidemenu"]] == "quit_app")
stopApp()
if (input[["sidemenu"]] == "new_proj"){
#inputs[["pr_path"]]("")
print("NEW project!!")
inputs[["pr_folder"]]("")
inputs[["pr_folder_std"]](.my_actual_wd)
inputs[["pr_name"]]("")
inputs[["pr_name_std"]]("")
inputs[["project_folder_std"]](.my_actual_wd)
project_folder <- list( "path"="", "root"="")
project_folder$path[[1]]<-""
project_folder$path <-
c(project_folder$path,
as.list(path_split(path_rel(inputs[["project_folder_std"]](),
start = roots_dir[[".."]]))[[1]]))
project_folder$root=".."
inputs[["project_folder"]](project_folder)
updateActionButton(session,"pr_folder", label=inputs[["pr_folder_std"]]())
updateTextInput(session,"pr_name", value=inputs[["pr_name_std"]]())
#inputs[["pr_path"]](.my_actual_wd) #not necessary
}
}, ignoreInit = TRUE)
# observe({
# if (input[["sidemenu"]] == "Small dataset") {
# inputs[["demo"]]("Small dataset")
# }
# if (input[["sidemenu"]] == "Melanoma dataset") {
# inputs[["demo"]]("Melanoma dataset")
# }
# })
save_tab <- function () {
if(!inputs[["project_loaded"]]()) {
showNotification("No porject created or loaded.", duration = 10, type = "warning")
return(NULL)
}
config_path <- file.path(inputs[["project_folder_std"]](), os_conf_subdir)
grep_str <- NULL
#browser()
if (input[["main_tabset"]] == "SC metadata") {
grep_str <- m_grep_str
config_file <- ".config_01_m.yml"
} else if (input[["main_tabset"]] == "Annotations") {
grep_str <- av_grep_str
config_file <- ".config_02_av.yml"
} else if (input[["main_tabset"]] == "Filters") {
grep_str <- thr_grep_str
config_file <- ".config_03_thr.yml"
} else if (input[["main_tabset"]] == "SC sampling depths") {
grep_str <- dp_grep_str
config_file <- ".config_04_dp.yml"
} else if (input[["main_tabset"]] == "Variants") {
grep_str <- va_grep_str
config_file <- ".config_05_va.yml"
} else if (input[["main_tabset"]] == "Inference") {
grep_str <- inf_grep_str
config_file <- ".config_06_inf.yml"
}
if (!is.null(grep_str)) {
doSave(grep_str, config_path, config_file)
showNotification(paste(input[["main_tabset"]], "configuration tab saved"),
duration = 10)
}
updateTabItems(session, "sidemenu", "hidden_menu")
}
load_tab <- function() {
if(!inputs[["project_loaded"]]()) {
showNotification("No porject created or loaded.", duration = 10, type = "warning")
return(NULL)
}
if(input[["main_tabset"]] == "Project")
return(NULL)
config_path <- file.path(inputs[["project_folder_std"]](), os_conf_subdir)
if (input[["main_tabset"]] == "SC metadata") {
m_doLoad_a(config_path)
m_doLoad_b()
} else if (input[["main_tabset"]] == "Annotations") {
av_doLoad_a(config_path)
uis <- av_dir_uis
for (i in av_dir_uis) {
av_doLoad_b(i)
}
} else if (input[["main_tabset"]] == "Filters") {
thr_doLoad_a(config_path)
uis <- thr_uis
for(i in thr_uis) {
thr_doLoad_b(i)
}
} else if (input[["main_tabset"]] == "SC sampling depths") {
dp_doLoad_a(config_path)
uis <- dp_uis
for(i in dp_uis) {
dp_doLoad_b(i)
}
} else if (input[["main_tabset"]] == "Variants") {
va_doLoad_a(config_path) #
uis <- va_uis
for(i in va_uis) {
va_doLoad_b(i)
}
va_doLoad_c()
} else if (input[["main_tabset"]] == "Inference") {
browser()
inf_doLoad_a(config_path)
uis <- inf_uis
for(i in uis) {
inf_doLoad_b(i)
}
inf_doLoad_c()
}
showNotification(paste(input[["main_tabset"]], "configuration tab loaded"), duration = 10)
updateTabItems(session, "sidemenu", "hidden_menu")
}
load_tabs <- function() {
if(!inputs[["project_loaded"]]()) {
showNotification("No porject created or loaded.", duration = 10, type = "warning")
return(NULL)
}
config_path <- file.path(inputs[["project_folder_std"]](), os_conf_subdir)
m_doLoad_a(config_path)
m_doLoad_b()
av_doLoad_a(config_path)
uis <- av_dir_uis
for (i in av_dir_uis) {
av_doLoad_b(i)
}
thr_doLoad_a(config_path)
uis <- thr_uis
for(i in thr_uis) {
thr_doLoad_b(i)
}
dp_doLoad_a(config_path)
uis <- dp_uis
for(i in dp_uis) {
dp_doLoad_b(i)
}
va_doLoad_a(config_path) #
uis <- va_uis
for(i in va_uis) {
va_doLoad_b(i)
}
va_doLoad_c()
browser()
inf_doLoad_a(config_path)
uis <- inf_uis
for(i in uis) {
inf_doLoad_b(i)
}
inf_doLoad_c()
showNotification(paste("project", "configuration reset to saved state"), duration = 10)
updateTabItems(session, "sidemenu", "hidden_menu")
}
catch_ui_files_priority = 1
observe({
save_ui_state(m_grep_str, "config_01_m.yml")
save_ui_state(av_grep_str, "config_02_av.yml")
save_ui_state(thr_grep_str, "config_03_thr.yml")
save_ui_state(dp_grep_str, "config_04_dp.yml")
save_ui_state(va_grep_str, "config_05_va.yml")
save_ui_state(inf_grep_str, "config_06_inf.yml")
},
priority = catch_ui_files_priority)
### End dashboard observers ####
update_proj_list <- function (project_folder) {
#browser()
os_conf_tmp <- file.path(path_home(), os_conf[[.Platform$OS.type]], "LACE")
if(dir.exists(os_conf_tmp)) {
if(file.exists(file.path(os_conf_tmp, "projects_list.yml")))
projects_list <- read.config(file = file.path(os_conf_tmp, "projects_list.yml"))
else
projects_list <- list()
}
else
projects_list <- list()
if(!is.list(projects_list))
projects_list <- list()
mask <- (projects_list %in% project_folder)
if (length(which(mask))>0) {
projects_list <- projects_list[-which(mask)]
}
if (!is.null(project_folder))
projects_list <- c(list(project_folder), projects_list)
names(projects_list) <- lapply(
seq_along(projects_list),
FUN = function(x) {
basename(projects_list[[x]])
})
write.config(config.dat = projects_list,
file.path = file.path(os_conf_tmp, "projects_list.yml"),
write.type = "yaml")
return(projects_list)
}
### Dashboard outputs ####
### End dashboard outputs ####
### Variational reactiveVals ####
va_uis <- c('va_depth_minimum',
'va_missing_values_max',
'va_minumum_median_total',
'va_minumum_median_mutation')
for (va_ui in va_uis)
inputs[[va_ui]] <- reactiveVal()
## inputs[['va_data_in_dir']] <- reactive(inputs[['thr_out_dir']]())
## dir <- out_subfolder_compute(inputs[['project_folder']](), 'filtered_var')
## inputs[['va_out_dir']] <- reactive(dir)
inputs[['va_verified_genes']] <- reactiveVal()
inputs[['va_list_genes']] <- reactiveVal()
## va_data_in_dir_ <- reactive(parseDirPath(roots=roots_dir, inputs[['va_data_in_dir']]()))
va_depth_minimum_ <-
reactive(inputs[['va_depth_minimum']]())
va_missing_values_max_ <-
reactive(inputs[['va_missing_values_max']]())
va_minumum_median_total_ <-
reactive(inputs[['va_minumum_median_total']]())
va_minumum_median_mutation_ <-
reactive(inputs[['va_minumum_median_mutation']]())
va_out_dir_ <-
reactive(parseDirPath(roots=roots_dir, inputs[['va_out_dir']]()))
va_non_NA_genes_ <- reactiveVal(NULL)
va_compute_output_ <- reactiveVal(NULL)
files_ <- reactiveVal(NULL)
list_genes_ <-
reactive(inputs[['va_list_genes']]())
verified_genes_ <-
reactive(inputs[['va_verified_genes']]())
va_rvs = reactiveValues(va_buttons = list(), va_observers = list())
### End variational reactiveVals ####
### Variational functions ####
va_exec <- function () {
#browser()
if (length(va_out_dir_()) == 0)
return()
if (!is.integer(inputs[['thr_out_dir']]()) &&
!is.integer(inputs[['dp_out_dir']]())) {
if (dir.exists(thr_out_dir_()) &&
dir.exists(dp_out_dir_())) {
#browser()
valid_genes_names <-
NA_compute(va_depth_minimum_(),
va_missing_values_max_(),
thr_out_dir_(),
dp_out_dir_(),
va_out_dir_(),
inputs[['m_time_points']]())
va_non_NA_genes_(valid_genes_names)
#browser()
files <- NA_compute2_load(thr_out_dir_(),
dp_out_dir_(),
va_out_dir_())
files_(files)
} else
showNotification(paste("Annotated VCF folder does not exist"),
duration = 10,
type = "warning")
} else
showNotification(paste("Annotated VCF folder is not set"),
duration = 10,
type = "warning")
}
va_exec2 <- function() {
req(inputs[['thr_out_dir']](), inputs[['dp_out_dir']]())
if (!is.integer(inputs[['thr_out_dir']]()) &&
!is.integer(inputs[['dp_out_dir']]()))
if (dir.exists(thr_out_dir_()) &&
dir.exists(dp_out_dir_()))
if (any(!sapply(files_(), is.null))){ # files not found
#browser()
NA_c2 <-
NA_compute2(va_depth_minimum_(),
va_minumum_median_total_(),
va_minumum_median_mutation_(),
thr_out_dir_(),
dp_out_dir_(),
va_out_dir_(),
inputs[['m_time_points']](),
verified_genes_(),
va_non_NA_genes_(),
files_())
#browser()
va_compute_output_(NA_c2$distinct_mutations)
#ggsave(file=file.path(inputs[["project_folder_std"]](),"D.svg"), plot=NA_c2$g, width=10, height=10)
output$va_filtered_bin_hmap <- renderPlot({
NA_c2$g
}, height = 600)
} else {
if (!is.null(files_()))
showNotification(paste("Files from previous steps not computed"),
duration = 10,
type = "warning")
} else
showNotification(paste("Sampling depth folder does not exist"),
duration = 10,
type = "warning")
else
showNotification(paste("Sampling depth folder is not set"),
duration = 10,
type = "warning")
}
### End variational functions ####
### Variational observers ####
observe({
va_rvs$observers =
lapply(va_uis,
function(i) {
observe({
req(inputs[[i]]())
})
}
)
},
priority = -1)
observeEvent(reactiveValuesToList(input), {
outs <- outputOptions(output)
lapply(names(outs),
function(name) {
outputOptions(output,
name,
suspendWhenHidden = FALSE)
})
},
once = TRUE,
priority = -1)
observe({
va_observers = lapply(va_uis,
function(i) {
observeEvent(input[[i]], {
## req(input)
inputs[[i]](input[[i]])
})
output[[i]] <- renderText(inputs[[i]]())
})
},
priority = -1)
observeEvent(inputs[['av_anovar_db_dir']](), {
#browser()
req(inputs[['av_anovar_db_dir']]())
## req(inputs[['thr_out_dir']](), inputs[['dp_out_dir']]())
## if (!is.integer(inputs[['thr_out_dir']]()) && !is.integer(inputs[['dp_out_dir']]())) {
if (!is.integer(inputs[['av_anovar_db_dir']]())) {
## if (dir.exists(thr_out_dir_()) && dir.exists(dp_out_dir_())) {
if (dir.exists(av_anovar_db_dir_())) {
## if (file.exists(file.path( thr_out_dir_(), "snpMut_filt_freq.rds"))){
fa_file <-
file_path_sans_ext(list.files(path = av_anovar_db_dir_(),
pattern = ".*.fa")[1])
ref_files <-
list.files(path = av_anovar_db_dir_(),
pattern = ".*.[^f][^a]")
ref_files2 <-
file_path_sans_ext(ref_files)
ref_files2 <-
ref_files[str_detect(fa_file, ref_files2)]
ref_files2 <-
ref_files2[which.min(str_length(ref_files2))]
ref_files2 <-
file.path(av_anovar_db_dir_(), ref_files2)
if (length(file.exists(ref_files2))>0) {
if (file.exists(ref_files2)) {
ref_info <-
read.table(file = ref_files2,
header = FALSE,
sep = '\t',
stringsAsFactors = FALSE)
list_gene_symbols <- ref_info[, 13]
## if (file.exists(file.path( av_anovar_db_dir_(), "snpMut_filt_freq.rds"))){
## print('LOAD FILE2')
## snpMut_filt_freq <- readRDS(file=paste0(file.path( thr_out_dir_(), "snpMut_filt_freq.rds")))
## print(head(snpMut_filt_freq))
} else {
showNotification(paste("annovar reference file",
ref_files2,
"not found"),
duration = 10,
type = "warning")
}
}
#not necessary
if (file.exists(file.path( va_out_dir_(), "snpMut_filt_freq_reduced.rds"))) {
snpMut_filt_freq <- readRDS(file=paste0(file.path( va_out_dir_(), "snpMut_filt_freq_reduced.rds")))
inputs[['va_list_genes']](sort(unique(snpMut_filt_freq$Gene)))
} else
inputs[['va_list_genes']](list_gene_symbols)
updateSelectizeInput(session,
'va_verified_genes',
choices = inputs[['va_list_genes']](),
selected = inputs[['va_verified_genes']](),
server = TRUE)
}
}
})
observeEvent(input[['va_verified_genes']], {
#req(input[['va_verified_genes']])
#browser()
inputs[['va_verified_genes']](input[['va_verified_genes']])
}, ignoreNULL = FALSE)
va_iv <- InputValidator$new()
va_iv$add_rule("va_depth_minimum", sv_between(0,500))
va_iv$add_rule("va_missing_values_max", sv_between(0.,1.))
va_iv$add_rule("va_minumum_median_total", sv_between(0,500))
va_iv$add_rule("va_minumum_median_mutation", sv_between(0,500))
va_iv$enable()
observeEvent(input$va_exec,{
req(va_iv$is_valid())
#browser()
va_exec()
if (file.exists(file.path( va_out_dir_(), "snpMut_filt_freq_reduced.rds"))) {
snpMut_filt_freq <- readRDS(file=paste0(file.path( va_out_dir_(), "snpMut_filt_freq_reduced.rds")))
inputs[['va_list_genes']](sort(unique(snpMut_filt_freq$Gene)))
}
updateSelectizeInput(session,
'va_verified_genes',
choices = inputs[['va_list_genes']](),
selected = inputs[['va_verified_genes']](),
server = TRUE)
va_exec2()
#browser()
#print("a")
})
observeEvent({ c(#files_(),
va_depth_minimum_(),
va_missing_values_max_(),
va_minumum_median_total_(),
va_minumum_median_mutation_(),
verified_genes_()
)
},
{
va_exec()
va_exec2()
},
ignoreNULL = FALSE,
ignoreInit = TRUE)
### End Variational observers ####
### Variational outputs ####
output$va_out <-
DT::renderDT(va_compute_output_(), server = TRUE)
#output[['va_verified_genes']] <-
# renderText(inputs[['va_verified_genes']]())
#output[['va_list_genes']] <-
# renderPrint(inputs[['va_list_genes']]())
#output[['va_out_dir']] <-
# renderText(parseDirPath(roots = roots_dir,
# inputs[['va_out_dir']]()))
output[['va_filters']] <-
renderPrint({
list(va_data_in_dir = parseDirPath(roots=roots_dir,
inputs[['thr_out_dir']]()),
depth_minimum = inputs$va_depth_minimum(),
missing_values_max = inputs$va_missing_values_max(),
minumum_median_total = inputs$va_minumum_median_total(),
minumum_median_mutation = inputs$va_minumum_median_mutation(),
va_out_dir = parseDirPath(roots = roots_dir,
inputs[['va_out_dir']]()),
va_verified_genes = inputs[['va_verified_genes']]())
})
### End variational outputs ####
### Depth reactivaVals ####
dp_uis <- c('dp_samtools_exec_dir', 'dp_bam_dir')
dp_rvs = reactiveValues(dp_buttons = list(), dp_observers = list())
###
for (dir_ui in dp_uis) {
defaultPath <- ""
# if(dir_ui == "dp_samtools_exec_dir")
# defaultPath <- path_rel(dirname(Sys.which("samtools")), start = "..")
shinyDirChoose(input,
dir_ui,
roots = roots_dir,
filetypes = c('', 'txt'),
defaultPath = defaultPath,
defaultRoot = "..")
}
for (dp_ui in dp_uis)
inputs[[dp_ui]] <- reactiveVal()
inputs[['dp_mut_dir']] <-
reactive(inputs[['thr_out_dir']]())
## inputs[['dp_out_dir']] <- reactiveVal()
dp_samtools_exec_dir_ <-
reactive(parseDirPath(roots = roots_dir,
inputs[['dp_samtools_exec_dir']]()))
dp_samtools_ <-
reactive(file.path(dp_samtools_exec_dir_(),
'samtools'))
dp_bam_dir_ <-
reactive(parseDirPath(roots = roots_dir,
inputs[['dp_bam_dir']]()))
dp_out_dir_ <-
reactive(parseDirPath(roots = roots_dir,
inputs[['dp_out_dir']]()))
dp_mut_dir_ <-
reactive(parseDirPath(roots = roots_dir,
inputs[['dp_mut_dir']]()))
### End depth reactivaVals ####
### Depth observers ####
observe({
dp_rvs$observers =
lapply(dp_uis,
function(i) {
observe({
req(inputs[[i]]())
updateActionButton(session, i, label = set_dir_ui(i))
})
}
)
},
priority = -1)
observeEvent(reactiveValuesToList(input), {
outs <- outputOptions(output)
lapply(names(outs),
function(name) {
outputOptions(output,
name,
suspendWhenHidden = FALSE)
})
},
once = TRUE,
priority = -1)
## observeEvent(reactiveValuesToList(input),{
## lapply(dp_uis, function(i) {
## click(i)
## hide(paste0(i,'-modal'))
## delay(300,runjs(paste0("$('#",i,"-modal #sF-cancelButton').click()")))
## })
## },once = T, priority = -1)
observe({
dp_observers = lapply(dp_uis,
function(i) {
observeEvent(input[[i]], {
req(input)
inputs[[i]](input[[i]])
})
output[[i]] <-
renderText(parseDirPath(roots = roots_dir,
inputs[[i]]()))
}
)},
priority = -1)
observeEvent(dp_samtools_exec_dir_(), {
if (!is.integer(input[['dp_samtools_exec_dir']])) {
if (file.exists(dp_samtools_()))
showNotification(paste("found samtools"),
duration = 10,
type = "message")
else
showNotification(paste("samtools", 'not present in',
dp_samtools_exec_dir_()),
duration = 10,
type = "warning")
}
})
### End depth observers ####
### Depth functions ####
dp_exec <- function() {
if (length(dp_out_dir_()) == 0)
return()
Opt = list() # MA: Perche` maiuscolo il nome della variabile?
Opt$StoredFile <- file.path(config_path, ".config_04_dp.yml")
Opt$ActFile <- file.path(config_path, "config_04_dp.yml")
Opt$ExtraFiles = NULL
OutFiles <- c("final_data_depth.txt", "final_data_mut.txt")
chk_files <- ManyInSomeOut(dp_bam_dir_(),
InFilesMask = ".*.bam$",
OutDir=dp_out_dir_(),
OutFiles = OutFiles,
Opt = Opt)
InFilesToDo <- chk_files$InFilesToDo
## Use metadata if available
if (!is.integer(inputs[['sc_metadata_file']]())) {
if (file.exists(sc_metadata_label_())) {
if (inputs[['m_id_column']]() %in% colnames(sc_metadata_()))
InFilesToDo <-
InFilesToDo[str_split_fixed(InFilesToDo,
"\\.",
n = 2)[, 1] %in%
as.character(sc_metadata_()[[inputs[['m_id_column']]()]])]
else
showNotification(paste("no valid metadata id column"),
duration = 10,
type = "warning")
} else
showNotification(paste("no valid metadata file"), duration = 10, type = "warning")
} else
showNotification(paste("no valid metadata file"), duration = 10, type = "warning")
InFilesToDo <-
file.path(dp_bam_dir_(), chk_files$InFilesToDo)
OutFilesToRm <-
file.path(dp_out_dir_(), chk_files$OutFilesToRm)
if (!is.integer(inputs[['dp_samtools_exec_dir']]()) &
!is.integer(inputs[['dp_bam_dir']]()) &
!is.integer(inputs[['dp_mut_dir']]())) {
if (dir.exists(dp_samtools_exec_dir_()) &
file.exists(dp_samtools_()) &
dir.exists(dp_bam_dir_()) & dir.exists(dp_mut_dir_())) {
dp_compute(sc_metadata_(),
dp_bam_dir_(),
dp_samtools_(),
thr_out_dir_(),
dp_out_dir_(),
inputs[['m_id_column']](),
InFilesToDo,
OutFilesToRm)
## return(read_file(file.path(dp_out_dir_(), 'stdout.log')))
} else
showNotification(paste("one of the folders or executable does not exist"),
duration = 10,
type = "warning")
} else
showNotification(paste("one of the folders is not set"),
duration = 10,
type = "warning")
return("possible errors")
}
### End depth functions ####
### Depth outputs ####
output$dp_out <- eventReactive(input$dp_exec,{
dp_exec()
})
output[['dp_mut_dir']] <-
renderText(parseDirPath(roots = roots_dir,
inputs[['dp_mut_dir']]()))
output[['dp_par']] <-
renderPrint({
list(samtools =parseDirPath(roots = roots_dir,
inputs$dp_samtools_exec_dir()),
bam_dir = parseDirPath(roots = roots_dir,
inputs$dp_bam_dir()),
mut_dir = parseDirPath(roots = roots_dir,
inputs$dp_mut_dir()),
out_dir = parseDirPath(roots = roots_dir,
inputs$dp_out_dir())
)
})
### End depth outputs ####
### Threshold reactiveVals ####
thr_uis = c('thr_alleles_ratio',
'thr_maf',
'thr_freq',
'thr_accepted_var',
'thr_negleted_var')
###
thr_rvs = reactiveValues(thr_buttons = list(),
thr_observers = list())
for (thr_ui in thr_uis)
inputs[[thr_ui]] <- reactiveVal()
thr_alleles_ratio_ <-
reactive(inputs[['thr_alleles_ratio']]())
thr_maf_ <-
reactive(inputs[['thr_maf']]())
thr_freq_ <-
reactive(inputs[['thr_freq']]())
thr_out_dir_ <-
reactive(parseDirPath(roots = roots_dir,
inputs[['thr_out_dir']]()))
thr_vcf_in_dir_ <-
reactive(parseDirPath(roots = roots_dir,
inputs[['thr_vcf_in_dir']]()))
exonic_list <- list("frameshift insertion",
"frameshift deletion",
"frameshift block substitution",
"stopgain",
"stoploss",
"nonframeshift insertion",
"nonframeshift deletion",
"nonframeshift block substitution",
"nonsynonymous SNV",
"synonymous SNV",
"unknown")
### End threshold reactiveVals ####
### Threshold functions ####
thr_exec <- function() {
if (length(thr_out_dir_()) == 0)
return()
Opt = list()
Opt$StoredFile <- file.path(config_path, ".config_03_thr.yml")
Opt$ActFile <- file.path(config_path, "config_03_thr.yml")
Opt$ExtraFiles = NULL
## chk_files <- OneInOneOut( thr_vcf_in_dir_(), InFilesMask = ".*.exonic_variant_function$", thr_out_dir_(), OutExt = "anninput", Opt = Opt)
OutFiles <- c("cells_aggregate_info.rds",
"scMutInfo.rds",
"SNPInfo.rds",
"snpMut_filt_freq.rds"
)
chk_files <- ManyInSomeOut(thr_vcf_in_dir_(),
InFilesMask =
".*.exonic_variant_function$",
OutDir=thr_out_dir_(),
OutFiles = OutFiles,
Opt = Opt)
InFilesToDo <- chk_files$InFilesToDo
## use metadata if available
if (!is.integer(inputs[['sc_metadata_file']]())) {
if (file.exists(sc_metadata_label_())){
if (inputs[['m_id_column']]() %in% colnames(sc_metadata_()))
InFilesToDo <-
InFilesToDo[str_split_fixed(InFilesToDo,
"\\.",
n = 2)[, 1] %in%
as.character(sc_metadata_()[[inputs[['m_id_column']]()]])]
else
showNotification(paste("no valid metadata id column"),
duration = 10,
type = "warning")
} else
showNotification(paste("no valid metadata file"),
duration = 10,
type = "warning")
} else
showNotification(paste("no valid metadata file"),
duration = 10,
type = "warning")
InFilesToDo <-
file.path(thr_vcf_in_dir_(),
chk_files$InFilesToDo)
OutFilesToRm <-
file.path(thr_out_dir_(),
chk_files$OutFilesToRm)
if (!is.integer(inputs[['thr_vcf_in_dir']]())) {
if (dir.exists(thr_vcf_in_dir_())) {
## filter1_compute(thr_vcf_in_dir_(), sc_metadata_(), thr_alleles_ratio_(), thr_maf_(), thr_freq_(), thr_out_dir_(), m_id_column_(), m_time_column_())
filter1_compute(thr_vcf_in_dir_(),
sc_metadata_(),
thr_alleles_ratio_(),
thr_maf_(),
thr_freq_(),
thr_out_dir_(),
inputs[['m_id_column']](),
inputs[['m_time_column']](),
inputs[['thr_accepted_var']](),
InFilesToDo,
OutFilesToRm)
filter2_compute(thr_vcf_in_dir_(),
sc_metadata_(),
thr_alleles_ratio_(),
thr_maf_(),
thr_freq_(),
thr_out_dir_(),
m_id_column_(),
m_time_column_(),
InFilesToDo,
OutFilesToRm)
snpMut_filt_freq <- filter3_compute(
thr_vcf_in_dir_(),
sc_metadata_(),
thr_alleles_ratio_(),
thr_maf_(),
thr_freq_(),
thr_out_dir_(),
m_id_column_(),
m_time_column_(),
inputs[['m_time_points']](),
InFilesToDo,
OutFilesToRm)
inputs[['va_list_genes']](sort(unique(snpMut_filt_freq$Gene)))
updateSelectizeInput(session,
'va_verified_genes',
choices = inputs[['va_list_genes']](),
selected = inputs[['va_verified_genes']](),
server = TRUE)
return(read_file(file.path(thr_vcf_in_dir_(),
'stdout.log')))
} else
showNotification(paste("Filtered VCF folder does not exist"),
duration = 10,
type = "warning")
} else
showNotification(paste("Filtered VCF folder is not set"),
duration = 10,
type = "warning")
return("Possible errors") # MA: return or raise an error?
}
### End threshold functions ####
### Threshold observers ####
observe({
thr_rvs$observers = lapply(thr_uis,
function(i) {
observe({
req(inputs[[i]]())
## updateActionButton(session, i, label = set_dir_ui(i))
updateNumericInput(session, i, value = inputs[[i]]())
})
}
)
},
priority = -1)
observeEvent(reactiveValuesToList(input), {
outs <- outputOptions(output)
lapply(names(outs),
function(name) {
outputOptions(output,
name,
suspendWhenHidden = FALSE)
})
},
once = TRUE,
priority = -1)
## # observeEvent(reactiveValuesToList(input),{
## # lapply(thr_uis, function(i) {
## # click(i)
## # hide(paste0(i,'-modal'))
## # delay(300,runjs(paste0("$('#",i,"-modal #sF-cancelButton').click()")))
## # })
## # },once = T, priority = -1)
###
## #dir <- out_subfolder_compute(inputs[['project_folder']](),'filtered_vcf')
## #inputs[['thr_out_dir']] <- reactive(dir)
observe({
thr_observers = lapply(thr_uis,
function(i) {
observeEvent(input[[i]], {
req(input)
inputs[[i]](input[[i]])
})
output[[i]] <- renderPrint(inputs[[i]]())
}
)
},
priority = -1)
## Exonic ui
observeEvent(reactiveValuesToList(input), {
inputs[['thr_accepted_var']](exonic_list)
inputs[['thr_negleted_var']](NULL)
},
once = TRUE,
priority = -1)
#observeEvent(input[['thr_accepted_var']],
# {
#browser()
#print(input[['thr_accepted_var']])
#print(inputs[['thr_accepted_var']]())
# })
#observeEvent(inputs[['thr_accepted_var']](),
# {
#browser()
#print(input[['thr_accepted_var']])
#print(inputs[['thr_accepted_var']]())
# })
output$thr_bucket_var_list <-
renderUI({
## showNotification(paste("renderUI[['thr_bucket_var_list']]"), duration = NULL)
bucket_list_basic <-
bucket_list(
header = "Choose the variant functions for inferential analysis",
add_rank_list(
text = "Considered exonic variants",
labels = inputs[['thr_accepted_var']](),
input_id = "thr_accepted_var",
options = sortable_options(multiDrag = TRUE, disabled = !is.null(inputs[["demo"]]()))
),
add_rank_list(
text = "Neglected exonic variants",
labels = inputs[['thr_negleted_var']](),
input_id = "thr_negleted_var",
options = sortable_options(multiDrag = TRUE, disabled = !is.null(inputs[["demo"]]()))
),
group_name = "thr_bucket_var_list",
orientation = "horizontal",
options = sortable_options(disabled = !is.null(inputs[["demo"]]()))
)
x <-
tagList(
span() %>%
make_title_help_popover (
tags$b("Exonic variant function annotations"),
"List of exonic varian functions",
text[["thr_bucket_var_list"]],
server = TRUE
),
bucket_list_basic
)
if (loading_()) {
loaded_(TRUE)
}
x
})
thr_iv <- InputValidator$new()
thr_iv$add_rule("thr_alleles_ratio", sv_between(1,55))
thr_iv$add_rule("thr_maf", sv_between(0.01,0.5))
thr_iv$add_rule("thr_freq", sv_between(0.,1.))
thr_iv$enable()
### Threshold observers ####
### Threshold outputs ####
output[['thr_vcf_in_dir']] <-
renderText(parseDirPath(roots = roots_dir,
inputs[['thr_vcf_in_dir']]()))
output[['thr_out_dir']] <-
renderText(parseDirPath(roots = roots_dir,
inputs[['thr_out_dir']]()))
output[['thr_filters']] <-
renderPrint({
list(thr_vcf_in_dir = parseDirPath(roots = roots_dir,
inputs[['thr_vcf_in_dir']]()),
alleles_ratio = inputs$thr_alleles_ratio(),
maf = inputs$thr_maf(),
freq = inputs$thr_freq(),
thr_out_dir = parseDirPath(roots = roots_dir,
inputs[['thr_out_dir']]()) )
})
output$thr_out <- eventReactive(input$thr_exec, {
req(thr_iv$is_valid())
thr_exec()
})
### End threshold outputs ####
### Annotation reactiveVals ####
av_dir_uis= c('av_anovar_exec_dir',
'av_anovar_db_dir',
'av_vcf_in_dir')
for (dir_ui in av_dir_uis)
inputs[[dir_ui]] <- reactiveVal()
av_rvs = reactiveValues(av_buttons = list(), av_observers = list())
## #dir <- out_subfolder_compute(inputs[['project_folder']](),'vcf_out')
## #inputs[['av_vcf_out_dir']] <- reactive(dir)
av_anovar_exec_dir_ <-
reactive(parseDirPath(roots = roots_dir,
inputs[['av_anovar_exec_dir']]()))
av_anovar_convert_ <-
reactive(file.path(av_anovar_exec_dir_(),
'convert2annovar.pl'))
av_anovar_db_dir_ <-
reactive(parseDirPath(roots = roots_dir,
inputs[['av_anovar_db_dir']]()))
av_vcf_in_dir_ <-
reactive(parseDirPath(roots = roots_dir,
inputs[['av_vcf_in_dir']]()))
av_vcf_out_dir_ <-
reactive(parseDirPath(roots = roots_dir,
inputs[['av_vcf_out_dir']]()))
av_anovar_annot_ <-
reactive(file.path(av_anovar_exec_dir_(),
'annotate_variation.pl'))
### End annotation reactiveVals ####
### Annotation functions ####
set_dir_ui <- function(dir_id,
default_dir_label = 'Select folder',
input_var = inputs,
basedir = "..") { # replace with roots_dir
this_label <- default_dir_label
meta <- input_var[[dir_id]]()
## if (basedir %in% names(meta))
if (!is.null(meta))
if (!is.integer(meta))
if (dir.exists(parseDirPath(roots = roots_dir, meta)))
this_label <- parseDirPath(roots = roots_dir, meta)
return(this_label)
}
out_subfolder_compute <- function(out_dir_inp, sub_dir) {
if ('path' %in% names(out_dir_inp)) {
tmp <- out_dir_inp[['path']]
## tmp <- tmp[-length(tmp)]
out_dir_inp[['path']] <- c(tmp, sub_dir)
}
return (out_dir_inp)
}
av_exec <- function() {
if(length(av_vcf_out_dir_())==0)
return()
log2_print('av_exec', msg = "LACEview:")
log2_print(paste("av_vcf_out_dir_()", av_vcf_out_dir_()), msg = "LACEview:")
Opt = list()
Opt$StoredFile <- file.path(config_path,".config_02_av.yml")
Opt$ActFile <- file.path(config_path,"config_02_av.yml")
Opt$ExtraFiles = NULL
chk_files <- OneInOneOut(av_vcf_in_dir_(),
InFilesMask = ".*vcf$",
av_vcf_out_dir_(),
OutExt =
"anninput.exonic_variant_function",
Opt = Opt)
InFilesToDo <- chk_files$InFilesToDo
## Use metadata if available
if (!is.integer(inputs[['sc_metadata_file']]())) {
if (file.exists(sc_metadata_label_())){
if (inputs[['m_id_column']]() %in% colnames(sc_metadata_()))
InFilesToDo <-
InFilesToDo[str_split_fixed(InFilesToDo,
"\\.",
n = 2)[, 1] %in%
as.character(sc_metadata_()[[inputs[['m_id_column']]()]])]
else
showNotification(paste("no valid metadata id column"),
duration = 10,
type = "warning")
}
else
showNotification(paste("no valid metadata file"),
duration = 10,
type = "warning")
}
else
showNotification(paste("no valid metadata file"),
duration = 10,
type = "warning")
InFilesToDo <- file.path(av_vcf_in_dir_(),
chk_files$InFilesToDo)
OutFilesToRm <- file.path(av_vcf_out_dir_(),
chk_files$OutFilesToRm)
if (!is.integer(inputs[['av_anovar_exec_dir']]()) &
!is.integer(inputs[['av_anovar_db_dir']]()) &
!is.integer(inputs[['av_vcf_in_dir']]())
) {
if (dir.exists(av_anovar_exec_dir_()) &
file.exists(av_anovar_convert_()) &
file.exists(av_anovar_annot_()) &
dir.exists(av_anovar_db_dir_()) &
dir.exists(av_vcf_in_dir_())
) {
av_compute(av_anovar_convert_(),
av_anovar_annot_(),
av_anovar_db_dir_(),
av_vcf_in_dir_(),
av_vcf_out_dir_(),
InFilesToDo = InFilesToDo,
OutFilesToRm = OutFilesToRm)
return(read_file(file.path(av_vcf_out_dir_(),
'stdout.log')))
} else
showNotification(paste("one of the folders or executable does not exist"),
duration = 10,
type = "warning")
} else
showNotification(paste("one of the folders is not set"),
duration = 10,
type = "warning")
return("possible errors") # MA: CHECK THESE!!!! IS THE CHECK!!!
}
### End annotation functions ####
### Annotation observers ####
for (dir_ui in av_dir_uis) { #av_rvs$buttons???
defaultPath <- ""
# if(dir_ui == "av_anovar_exec_dir")
# defaultPath <- path_rel(Sys.which("annotate_variation.pl"), start = "..")
shinyDirChoose(input,
dir_ui,
roots = roots_dir,
defaultPath = defaultPath,
filetypes = c('', 'txt'),
defaultRoot = "..")
}
## Update buttons
observe({
av_rvs$observers = lapply(av_dir_uis,
function(i) {
observe({
req(inputs[[i]]())
updateActionButton(session,
i,
label = set_dir_ui(i))
})
}
)
## reactiveValuesToList(av_rvs)
},
priority = -1)
## Make ui updatable
observeEvent(reactiveValuesToList(input), {
outs <- outputOptions(output)
lapply(names(outs),
function(name) {
outputOptions(output,
name,
suspendWhenHidden = FALSE)
})
},
once = TRUE,
priority = -1)
## observeEvent(reactiveValuesToList(input), {
## lapply(av_dir_uis,
## function(i) {
## click(i)
## hide(paste0(i, '-modal'))
## delay(300,
## runjs(paste0("$('#",
## i,
## "-modal #sF-cancelButton').click()")))
## })
## #delay(1000, runjs("$('.sF-modal modal-dialog modal-lg').keydown(new KeyboardEvent('keydown', {'keyCode': 40}))"))
## #delay(1000,"$('#av_anovar_exec_dir-modal').dispatchEvent(new KeyboardEvent('keydown', {'keyCode': 40}))")
## #delay(1000,runjs("handleArrowKey('down')"))
## },
## once = T,
## priority = -1)
observe({
av_observers = lapply(av_dir_uis,
function(i) {
observeEvent(input[[i]], {
req(input)
inputs[[i]](input[[i]])
})
output[[i]] <-
renderText(parseDirPath(roots = roots_dir,
inputs[[i]]()))
}
)
## reactiveValuesToList(av_rvs)
},
priority = -1)
## observeEvent(inputs[['av_anovar_exec_dir']](),{
observeEvent(av_anovar_exec_dir_(), {
if (!is.integer(input[['av_anovar_exec_dir']])) {
if (file.exists(av_anovar_convert_()))
showNotification(paste("found convert2annovar.pl"),
duration = 10,
type = "message")
else
showNotification(paste("convert2annovar.pl",
'not present in',
av_anovar_exec_dir_()),
duration = 10,
type = "warning")
if (file.exists(av_anovar_annot_()))
showNotification(paste("found annotate_variation.pl"),
duration = 10,
type = "message")
else
showNotification(paste("annotate_variation.pl",'not present in',
av_anovar_exec_dir_()),
duration = 10,
type = "warning")
}
})
output$av_out <- eventReactive(input$av_exec, {
av_exec()
},
ignoreInit = TRUE)
### End annotation observers ####
### Annotation outputs ####
output[['av_vcf_out_dir']] <-
renderText(parseDirPath(roots = roots_dir,
inputs[['av_vcf_out_dir']]()))
output$av_anovar_convert <-
renderText(av_anovar_convert_())
output$av_anovar_annot <-
renderText(av_anovar_annot_())
### End annotation outputs ####
### Metadata reactiveVals ####
loaded_input_ <- reactiveVal(list())
loaded_ <- reactiveVal(FALSE)
m_widgetId_ <- reactiveVal()
loaded_input <- list()
initialInputs <- list()
initialInputs_copy <- list()
the_files <- list()
### End metadata reactiveVals ####
### Metadata observers ####
## add types to ui #remove
observeEvent(input, {
initialInputs <<- reactiveValuesToList(input) # MA: WTF! Ma decidersi sugli assegnamenti????
for (inp in names(initialInputs)) {
## print(inp)
runjs(getWidgetType(inp))
## print(input$inputType)
}
},
once = TRUE,
priority = 5)
## Get types #remove
observe({
types <- list()
for (inp in names(initialInputs))
types[[inp]]<-input[[paste0('inputType_',inp)]]
types_(types)
},
priority = 4)
#####
#####
## widgetId output
observe({
reactiveValuesToList(input)
types<-types_()
for (n in names(initialInputs_copy)) {
if (n %in% names(types))
if (types[[n]] == 'shinyFiles')
if (n %in% names(the_files)) {
## initialInputs_copy[[n]] <<- the_files[[n]]
}
}
m_widgetId_(initialInputs_copy)
},
priority = catch_ui_files_priority - 1)
output$m_widgetId <- renderPrint({
m_widgetId_()
})
shinyFileChoose(input,
'sc_metadata_file',
roots = roots_dir,
filetypes = c('rds',''),
defaultRoot = "..")
## Set_ui_files
set_file_ui <- function(dir_id,
default_dir_label = 'Select file',
input_var = inputs,
basedir = "..") { #replace with roots_dir
this_label <- default_dir_label
meta <- input_var[[dir_id]]()
## if (basedir %in% names(meta))
if (!is.null(meta))
if (!is.integer(meta))
if (file.exists(as.character(parseFilePaths(roots = roots_dir,
meta)[['datapath']])))
this_label <- as.character(parseFilePaths(roots = roots_dir,
meta)[['datapath']])
## showNotification(this_label, duration = 10)
return(this_label)
}
## # output$m_sc_metadata_col <- reactive({
## # if (length(sc_metadata_())>0) {
## # sc_metadata_col <- colnames(sc_metadata_())
## # } else {
## # sc_metadata_col <- c("")
## # }
## # sc_metadata_col
## # })
#####
m_dir_uis = c('sc_metadata_file',
'm_time_column',
'm_time_points',
'm_id_column')
## inputs <- list()
for (dir_ui in m_dir_uis)
inputs[[dir_ui]] <- reactiveVal()
loading_ <- reactiveVal(FALSE)
loaded_ <- reactiveVal(FALSE)
#####
sc_metadata_label_ <- reactiveVal("")
sc_metadata_ <- reactiveVal()
choices_ <- reactiveVal()
observeEvent(input[['sc_metadata_file']],{
if (! loading_()) {
## showNotification(paste("input[['sc_metadata_file']]","inputs[['sc_metadata_file']](input[['sc_metadata_file']])"), duration = NULL)
inputs[['sc_metadata_file']](input[['sc_metadata_file']])
## print("set_file_ui('sc_metadata_file')")
## print(set_file_ui('sc_metadata_file'))
sc_metadata_label_(set_file_ui('sc_metadata_file'))
if (file.exists(sc_metadata_label_()) ) {
if (file_ext(sc_metadata_label_()) %in% c("rds", "RDS") ) {
cellInfo <- readRDS( sc_metadata_label_() )
if (!is.data.frame(cellInfo)){
showNotification("No metadata file",
type = "warning",
duration = 10)
cellInfo <- data.frame()
}
} else
cellInfo <- fread(sc_metadata_label_(), header=TRUE, data.table=FALSE)
} else {
showNotification("No metadata file",
type = "warning",
duration = 10)
# hideTab(inputId = "main_tabset",
# target = "Annotations")
# hideTab(inputId = "main_tabset",
# target = "Filters")
# hideTab(inputId = "main_tabset",
# target = "SC sampling depths")
# hideTab(inputId = "main_tabset",
# target = "Variants")
# hideTab(inputId = "main_tabset",
# target = "Inference")
# hideTab(inputId = "main_tabset",
# target = "Results")
cellInfo <- data.frame()
}
sc_metadata_(cellInfo)
if ( file.exists(sc_metadata_label_()) )
choices_(colnames(sc_metadata_()))
else
choices_(c(""))
id_col <- NULL
time_col <- NULL
if (length(choices_()) > 2) {
id_col <- choices_()[1]
time_col <- choices_()[2]
}
inputs[['m_id_column']](id_col)
inputs[['m_time_column']](time_col)
time_points <- NULL
if (!is.null(time_col))
time_points <- unique(as.character(sc_metadata_()[, time_col]))
inputs[['m_time_points']](time_points)
}
})
observeEvent(input[['m_id_column']], {
if (! loading_()) {
## showNotification(paste("input[['m_time_column']]","inputs[['m_time_column']](input[['m_time_column']])"), duration = NULL)
id_col <- input[['m_id_column']]
inputs[['m_id_column']](id_col)
if ((inputs[['m_time_column']]() == inputs[['m_id_column']]()) &&
!("" == inputs[['m_id_column']]()))
showNotification(paste("Same column for cell Id and time"),
type = "warning",
duration = 10)
## # id_points <- NULL
## # if ( id_col %in% colnames(sc_metadata_()) )
## # id_points <- unique(as.character(sc_metadata_()[, id_col]))
## # inputs[['m_id_points']](id_points)
}
})
observeEvent(input[['m_time_column']], {
if (! loading_()) {
time_col <- input[['m_time_column']]
inputs[['m_time_column']](time_col)
time_points <- NULL
if (time_col %in% colnames(sc_metadata_()) )
time_points <- unique(as.character(sc_metadata_()[, time_col]))
inputs[['m_time_points']](time_points)
if ((inputs[['m_time_column']]() == inputs[['m_id_column']]()) &&
!(""==inputs[['m_time_column']]()))
showNotification(paste("Same column for cell Id and time"),
type = "warning",
duration = 10)
}
})
observeEvent(input[['m_time_points']], {
if (! loading_()) {
inputs[['m_time_points']](input[['m_time_points']])
}
if (loading_() & loaded_()) {
loading_(FALSE)
loaded_(FALSE)
}
if (file.exists(sc_metadata_label_()) )
if (!is.null(input[['m_time_points']]))
if (length(input[['m_time_points']]) > 1) {
# showTab(inputId = "main_tabset",
# target = "Annotations")
# showTab(inputId = "main_tabset",
# target = "Filters")
# showTab(inputId = "main_tabset",
# target = "SC sampling depths")
# showTab(inputId = "main_tabset",
# target = "Variants")
# showTab(inputId = "main_tabset",
# target = "Inference")
}
})
observeEvent(input[["pr_next"]],{ # The previous does not trigger the event for consecutive load
if ( file.exists(sc_metadata_label_()) )
if (!is.null(input[['m_time_points']]))
if (length(input[['m_time_points']]) > 1) {
# showTab(inputId = "main_tabset",
# target = "Annotations")
# showTab(inputId = "main_tabset",
# target = "Filters")
# showTab(inputId = "main_tabset",
# target = "SC sampling depths")
# showTab(inputId = "main_tabset",
# target = "Variants")
# showTab(inputId = "main_tabset",
# target = "Inference")
}
# delay(1000,
# updateTabsetPanel(session, "main_tabset", selected = "SC metadata")
# )
})
observeEvent(inputs[['sc_metadata_file']](), {
## update the file select button name
## showNotification(paste("inputs[['sc_metadata_file']]","updateActionButton"), duration = NULL)
updateActionButton(session,
'sc_metadata_file',
label = set_file_ui('sc_metadata_file'))
})
### problema update ma necessario
observeEvent(inputs[['m_time_column']](), {
## update time_col ui
## showNotification(paste("inputs[['m_time_column']]","updateSelectInput"), duration = NULL)
updateSelectInput(session,
"m_time_column",
## label = "Time column",
choices = choices_(),
selected = inputs[['m_time_column']]()
)
})
observeEvent(inputs[['m_id_column']](),{
## Update time_col ui
## showNotification(paste("inputs[['m_time_column']]","updateSelectInput"), duration = NULL)
updateSelectInput(session,
"m_id_column",
## label = "Cell id column",
choices = choices_(),
selected = inputs[['m_id_column']]()
)
})
######
observe({
hide(id = "m_idCol_div")
if (file.exists(sc_metadata_label_()) ) {
shinyjs::show(id="m_idCol_div")
}
})
observe({
hide(id = "m_timePointsCol_div")
if (file.exists(sc_metadata_label_()) ) {
shinyjs::show(id="m_timePointsCol_div")
}
})
## Time_column ui
output$m_idCol <-
renderUI(selectInput("m_id_column", "Cell id column", c("")) %>%
make_shiny_help_popover ("Ids column",
text[["m_idCol"]],
server = TRUE
)
)
output$m_timePointsCol <-
renderUI(selectInput("m_time_column", "Time column", c("")) %>%
make_shiny_help_popover ("Sampling times column",
text[["m_timePointsCol"]],
server = TRUE
)
)
## Time_points ui
output$m_timePoints <-
renderUI({
rank_list_basic <-
rank_list(text = "Drag the time points in chronological order (before the smaller times)",
labels = inputs[['m_time_points']](),
input_id = "m_time_points",
options = sortable_options(disabled = !is.null(inputs[["demo"]]()))
)
x <- rank_list_basic %>%
make_title_help_popover (tags$b("Sampling points"),
"Sampling time points",
text[["m_timePoints"]],
server = TRUE
)
if (loading_()) {
loaded_(TRUE)
}
x
})
observe({
hide(id = "m_timePoints_div")
if (file.exists(sc_metadata_label_()) )
shinyjs::show(id = "m_timePoints_div")
})
## output[['sc_metadata_file']] <- renderText(parseFilePaths(roots = roots_dir, inputs[['sc_metadata_file']]()))
output[['m_id_column_tab']] <-
renderTable(head(sc_metadata_()[inputs[['m_id_column']]()]),
bordered = TRUE,
rownames = TRUE)
output[['sc_metadata_file']] <-
renderPrint(inputs[['sc_metadata_file']]())
output[['m_time_column']] <-
renderText(inputs[['m_time_column']]())
output[['m_id_column']] <-
renderText(inputs[['m_id_column']]())
output[['m_time_points']] <-
renderText(inputs[['m_time_points']]())
## #output[['m_id_column']] <- renderPrint(inputs[['m_id_column']]())
## #output$cellInfo <- renderTable({
## # if ('root'%in%names(input$sc_metadata_file)){
## # inFile <- parseFilePaths(roots = roots_dir[input$sc_metadata_file[['root']]], input$sc_metadata_file)
## # if ( nrow(inFile)) {
## # #cellInfo <- read.csv(as.character(inFile$datapath))
## # cellInfo <- readRDS(as.character(inFile$datapath))
## # }
## # }
## #})
outputOptions(output, "m_timePoints", suspendWhenHidden = FALSE)
outs <- outputOptions(output)
lapply(names(outs),
function(name) {
outputOptions(output,
name,
suspendWhenHidden = FALSE)
})
#rs_(callr::r_session$new(options = sopt, wait = T))
#rs_()$supervise(T)
# rp <- callr::r_bg(
# func = long_job,
# args = list("port"=port),
# supervise = TRUE
#)
observeEvent(input[["res_refresh"]], {
#browser()
returned_vals <- show_result(rs_())
rs_(returned_vals$rs)
inputs[["res_lastrefresh"]](returned_vals$message)
})
output[["res_lastrefresh"]] <- renderText(inputs[["res_lastrefresh"]]())
}
shinyApp(ui, server)
## return (shinyApp(ui, server))
## runApp(system.file("shiny", "tooltip_popover_modal", package = "bsplus"))
##}
### end of file -- app.R
BIMIB-DISCo/LACE documentation built on April 24, 2024, 7:22 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
### app.R --
###
### Main LACEinterface file.
###
### See file LICENSE in the main folder for licensing and copyright
### information.
### reactlogShow(time = FALSE)
### Libraries needed by the app.
suppressMessages(library(biomaRt, exclude = c("show", "select")))
suppressMessages(library(foreach))
suppressMessages(library(doParallel))
suppressMessages(library(sortable))
suppressMessages(library(shiny,
exclude = c("runExample",
"dataTableOutput",
"renderDataTable",
"validate",
"show")))
suppressMessages(library(shinythemes))
suppressMessages(library(dplyr))
suppressMessages(library(forcats))
suppressMessages(library(tidyr))
suppressMessages(library(readr))
suppressMessages(library(shinyFiles))
suppressMessages(library(shinyjs, exclude = c("show")))
## library(shinyBS)
suppressMessages(library(jsonlite))
suppressMessages(library(configr))
## library(readr)
suppressMessages(library(DT))
suppressMessages(library(stringr))
suppressMessages(library(tools))
suppressMessages(library(fs))
suppressMessages(library(data.table, exclude = c("first", "last", "between")))
suppressMessages(library(htmltools))
suppressMessages(library(shinyBS))
suppressMessages(library(bsplus))
suppressMessages(library(shinydashboard))
suppressMessages(library(shinyvalidate))
suppressMessages(library(logr))
suppressMessages(library(ggplot2))
suppressMessages(library(svglite))
#library(widgetframe)
### Code
### ====
### getWidgetType --
getWidgetType <- function(widgetId) {
paste0("elem = document.getElementById('", widgetId, "');
var message;
if (elem == null) {
message = 'None'
} else {
// RStudio Viewer + IE workaround (dont have .include())
if (elem.getAttribute('class').indexOf('js-range-slider') > -1) {
message = 'slider'
} else if (elem.getAttribute('class').indexOf('shinyFiles') > -1) {
message = 'shinyFiles'
} else if (elem.getAttribute('class').indexOf('shinyDirectories') > -1) {
message = 'shinyDirectories'
} else if (elem.nodeName == 'SELECT') {
message = 'select'
} else if (elem.getAttribute('class').indexOf('shiny-text-output') > -1) {
message = 'shiny-text-output'
} else if (elem.getAttribute('class').indexOf('selectized') > -1) {
message = 'selectized'
} else {
message = elem.getAttribute('type');
}
}
Shiny.onInputChange('inputType_", widgetId,"', message)
"
)
}
### jsCode --
jsCode <- "shinyBS.addTooltip = function(id, type, opts) {
var $id = shinyBS.getTooltipTarget(id);
var dopts = {html: true};
opts = $.extend(opts, dopts);
if (type == 'tooltip') {
$id.tooltip('destroy');
setTimeout(function() { $id.tooltip(opts); }, 200);
} else if(type == 'popover') {
$id.popover('destroy');
setTimeout(function() { $id.popover(opts); }, 200);
}
}"
log2_print <- function(x, msg = "") {
if (str_length(msg)>0)
log_print(msg, console = FALSE, blank_after = FALSE, hide_notes =TRUE)
log_print(x, console = FALSE, blank_after = FALSE, hide_notes =FALSE)
}
#log2_print <- function(x, msg = "") {}
### compare_named_lists --
###
### Notes:
### MA: Seems a bit complicated. What is this supposed to do?
compare_named_lists <- function(l1, l2) {
if (is.list(l1) && is.list(l2)) { # if they are lists
if (length(unique(names(l1))) == length(l1) &&
length(unique(names(l2))) == length(l2) &&
!("" %in% names(l1)) &&
!("" %in% names(l2))
) { # if they are named
st <- TRUE
for (i in unique(c(names(l1), names(l2)))) {
## If the same name is present in both..
##
## Notes:
## MA: are we sure there is no 'intersection' operation on
## lists in R?
if (i %in% names(l1) && i %in% names(l2)) {
if (is.list(l1[[i]]))
st <- st && compare_named_lists(l1[[i]], l2[[i]])
else
st <- st && identical(l1[[i]], l2[[i]])
}
else
return(FALSE)
}
return(st)
}
return(FALSE)
}
else
return(FALSE)
}
### Help Management
### ===============
source("info_help.R")
### make_shiny_help_popover --
make_shiny_help_popover <- function(for_object,
pop_title,
pop_text,
with_icon = shiny_iconlink(),
server = FALSE) {
with_icon <- with_icon %>%
bs_embed_popover(title = pop_title,
content = pop_text,
placement = "right",
trigger = "hover",
delay = list("show" = 200, "hide" = 3000),
html = TRUE
)
for_object <- for_object %>% shinyInput_label_embed(with_icon)
if (server)
for_object <-
tagList(for_object,
tags$script("$(function () {$('[data-toggle=\"popover\"]').popover()})")
)
return(for_object)
}
### make_title_help_popover
make_title_help_popover <- function(for_object,
near_label,
pop_title,
pop_text,
with_icon = shiny_iconlink(),
server = FALSE) {
with_icon <- with_icon %>%
bs_embed_popover(title = pop_title,
content = pop_text,
placement = "right",
trigger = "hover",
delay= list("show"= 200, "hide"= 3000),
html = TRUE
)
with_icon <- htmltools::div(class = "pull-right", with_icon)
tag <- htmltools::div(class = "form-group shiny-input-container",
near_label,
br(),
for_object)
tag$children[[1]] <-
tag$children[[1]] %>%
htmltools::tagAppendChild(with_icon) %>%
htmltools::tagAppendAttributes(style = "width:100%;")
if (server)
tag <-
tagList(tag,
tags$script("$(function () {$('[data-toggle=\"popover\"]').popover()})")
)
return(tag)
}
### inline --
inline = function (x) {
tags$div(style="display:inline-block;", x)
}
### ui -- ####
ui <- fluidPage(
## singleton(tags$head(tags$script(src = "bs.js"))),
useShinyjs(),
withMathJax(),
## extendShinyjs(text = jsCode, functions = c("addTooltip")),
## extendShinyjs(text = jsCode, functions = c("bsPopover")),
tags$head(tags$style("@import url(https://use.fontawesome.com/releases/v5.7.2/css/all.css);"),
tags$style(HTML(".bucket-list-container {min-height: 290px; max-height: 300px;}")),
tags$style(HTML(".rank-list {min-height: 100px; max-height: 240px; overflow-y: scroll;}")),
#tags$style(HTML(".shinyDirectories, .shinyFiles { width: 100%; direction: rtl; white-space: nowrap; overflow: hidden; text-overflow: ellipsis;}")),
tags$style(HTML(".shinyDirectories, .shinyFiles { width: 100%; white-space: nowrap; overflow: hidden; text-overflow: ellipsis;}")),
tags$style(type="text/css", "body {padding-bottom: 70px;}"),
tags$style(HTML(".content-wrapper, .right-side {background-color: #ffffff;}"))
),
use_bs_popover(),
dashboardPage(
dashboardHeader(
title = "LACE 2.0",
tags$li(class = "dropdown",
tags$a(uiOutput("pr_title_ui_h")
)
)
),
dashboardSidebar(
sidebarMenu( id = "sidemenu",
hidden(menuItem("hidden_menu31", tabName = "hidden_menu31")),
menuItem(
"Application",
tabName = "application",
icon = icon("braille"), #icon("window-maximize"),
hidden(menuItem("hidden_menu3", tabName = "hidden_menu3")),
menuSubItem("New Project", tabName = "new_proj", icon = icon("layer-group") ),
menuSubItem("Quit", tabName = "quit_app", icon = icon("power-off") )#,
#actionButton("quit_app", "Quit")
),
hidden(menuItem("hidden_menu", tabName = "hidden_menu")),
menuItem(
"Projects",
tabName = "Projects",
icon = icon("cubes"),
#expandedName = "ttt",
menuItemOutput("recent_projects"),
hidden(menuItem("hidden_menu2", tabName = "hidden_menu2")),
# menuItem(
# "Recent Projects",
# tabName = "Recent Projects",
# icon = icon("th"),
# #expandedName = "projects",
# menuSubItem(
# "test22",
# tabName = ",media,disco,work_folder,Downloads,gitlace,LACEinterface,test2",
# #icon = icon("th"),
# #inline(actionButton("save_tab", "save")),
# #inline(actionButton("load_tab", "load"))
# ),
# menuSubItem(
# "test2",
# tabName = ",media,disco,work_folder,Downloads,gitlace,LACEinterface,test2",
# #icon = icon("th"),
# #inline(actionButton("save_tab", "save")),
# #inline(actionButton("load_tab", "load"))
# )#,
# #hidden(menuItem("hidden_menu4", tabName = "hidden_menu4"))
# ),
menuItem(
"Demo Projects",
tabName = "Demo Projects",
icon = icon("database"),
#expandedName = "demos",
menuSubItem(
"Melanoma dataset (Rambow)",
tabName = "Melanoma dataset",
#icon = icon("th"),
#inline(actionButton("save_tab", "save")),
#inline(actionButton("load_tab", "load"))
),
menuSubItem(
"Small dataset",
tabName = "Small dataset",
#icon = icon("th")#,
#inline(actionButton("save_tab", "save")),
#inline(actionButton("load_tab", "load"))
)#,
#hidden(menuItem("hidden_menu3", tabName = "hidden_menu3"))
)#,
#hidden(menuItem("hidden_menu1", tabName = "hidden_menu1"))
),
menuItem(
"Current Project",
tabName = "dashboard",
icon = icon("cube"),
hidden(menuItem("hidden_menu2", tabName = "hidden_menu2")),
#menuSubItem("Close Project", tabName = "close_proj", icon = icon("times-circle") ),
#actionButton("close_proj", "Close Project"),
menuItem(
"Save and Load Current Tab",
tabName = "dashboard_save",
icon = icon("th"),
hidden(menuItem("hidden_menu_SLpre", tabName = "hidden_menu_SLpre")),
menuSubItem("Save", tabName = "save_tab", icon = icon("download") ),
menuSubItem("Load", tabName = "load_tab", icon = icon("upload") ),
menuSubItem("Reset project", tabName = "load_tabs"),
hidden(menuSubItem("hidden_menu_SL", tabName = "hidden_menu_SL"))
#inline(actionButton("save_tab", "Save")),
#inline(actionButton("load_tab", "Load"))
)
)#,
#,
# menuItem(
# "Save and Load All Tabs",
# tabName = "dashboard",
# icon = icon("th"),
# inline(actionButton("save_tab", "save")),
# inline(actionButton("load_tab", "load"))
# ),
# menuItem(
# "Reset Tabs",
# tabName = "dashboard",
# icon = icon("th"),
# inline(actionButton("save_tab", "Clean and restore "))
# )
),
collapsed = FALSE
),
dashboardBody(
tabItems(
tabItem(tabName = "hidden_menu"),
tabItem(tabName = "Small dataset"),
tabItem(tabName = "Melanoma dataset"),
tabItem(tabName = "test22"),
tabItem(tabName = "test2")
),
div(id = "computation_idCol_div",
h3("Processing ... please wait")
),
fluidRow(
column(width = 12,
tabsetPanel(id = "main_tabset",
type = "tabs",
## Project tab
tabPanel(
"Project",
br(),
uiOutput("pr_title_ui"),
br(),
helpText(text[["pr_tab_help"]]),
br(),br(),
shinyDirButton('pr_folder',
'Select folder',
'Please select the project root folder', FALSE) %>%
make_title_help_popover (
tags$b("Project root folder"),
"Project folder",
text[["pr_folder"]]
),
br(),
textInput("pr_name",
"Name",
placeholder = "Your project name") %>%
make_shiny_help_popover(
"Project name",
text[["pr_name"]]
),
br(),br(),
div(id = "pr_path_div",
uiOutput("pr_path_ui")
),
actionButton("pr_next", "Create project"),
br(),br(),
),
## Metadata tab
tabPanel(
"SC metadata",
br(),
tags$h3("Single cell metadata info"),
br(),
helpText(text[["m_tab_help"]]),
br(), br(),
shinyFilesButton('sc_metadata_file',
'Select file',
'Please select the experiment metadata file', FALSE) %>%
make_title_help_popover (
tags$b("Metadata file"),
"Metadata info file",
text[["sc_metadata_file"]],
server = TRUE
),
br(),
br(),
div(id = "m_idCol_div",
uiOutput("m_idCol")
),
tableOutput("m_id_column_tab"),
br(),
div(id="m_timePointsCol_div",
uiOutput("m_timePointsCol")
),
div(id="m_timePoints_div",
uiOutput("m_timePoints")
),
br(), br(),
),
## Annotation tab
tabPanel(
"Annotations",
br(),
tags$h3("Gene variant annotations"),
br(),
helpText(text[["av_tab_help"]]),
br(), br(),
## runjs(jsCode),
shinyDirButton('av_anovar_exec_dir',
'Select folder',
'Please select Annovar executable folder',
FALSE) %>%
make_title_help_popover (
tags$b("Annovar executable folder"),
"Annovar",
text[["av_anovar_exec_dir"]]
),
br(),
br(),
shinyDirButton('av_anovar_db_dir',
'Select folder',
'Please select Annovar reference database folder',
FALSE) %>%
make_title_help_popover (
tags$b("Annovar reference database"),
"Annovar reference database",
text[["av_anovar_db_dir"]]
),
br(),
br(),
shinyDirButton('av_vcf_in_dir',
'Select folder',
'Please select VCF folder',
FALSE) %>%
make_title_help_popover (
tags$b("Variant calling files folder"),
"Variant calling files folder",
text[["av_vcf_in_dir"]]
),
br(),
br(),
## tags$b("Output folder"),
## br(),
## shinyDirButton('av_out_dir', 'Select folder', 'Please select output folder', FALSE),
br(),
br(),
tags$b("Run"),
br(),
actionButton("av_exec",
"Annotate variants"),
# tags$span(icon("info-circle"),
# id = "icon_av_exec",
# style = "color: blue;"),
# bsPopover("icon_av_exec",
# "Load inputs",
# text[["av_exec"]],
# placement = "right",
# trigger = "hover",
# options = list("delay': {show : 500, hide : 2000}, 'a" = "show")),
br(),br(),
## tags$b("Result"),
## br(),
## verbatimTextOutput("av_anovar_exec_dir"),
## verbatimTextOutput("av_anovar_db_dir"),
## verbatimTextOutput("av_vcf_out_dir")
),
## Filters tab
tabPanel(
"Filters",
br(),
tags$h3("Quality filters"),
br(),
helpText(text[["thr_tab_help"]]),
br(), br(),
numericInput(
inputId = "thr_alleles_ratio",
label = "Alternate frequency",
min = 1,
max = 500,
step = 1,
value = 2
) %>%
make_shiny_help_popover(
"Cell alternate allele frequency",
text[["thr_alleles_ratio"]]
),
numericInput(
inputId = "thr_maf",
label = "MAF",
min = 0.01,
max = 0.5,
step = 0.005,
value = 0.01
) %>%
make_shiny_help_popover(
"Minor alleles frequency",
text[["thr_maf"]]
),
numericInput(
inputId = "thr_freq",
label = "Variant frequency",
min = 0.,
max = 1,
step = 0.01,
value = 0.01
) %>%
make_shiny_help_popover(
"Sample variant frequency",
text[["thr_freq"]]
),
br(),
div(id = "thr_bucket_var_list_div",
uiOutput("thr_bucket_var_list")
),
br(),br(),br(),br(),
tags$b("Run"),
br(),
actionButton("thr_exec", "Apply filters"),
br(),br(),
## tags$b("Result"),
## verbatimTextOutput("thr_filters"),
## verbatimTextOutput('thr_accepted_var'),
## verbatimTextOutput('thr_negleted_var')
),
## Depth tab
tabPanel(
"SC sampling depths",
br(),
tags$h3("Single cell sampling depth"),
br(),
helpText(text[["dp_tab_help"]]),
br(), br(),
shinyDirButton('dp_samtools_exec_dir',
'Select folder',
'Please select samtools executable folder',
FALSE) %>%
make_title_help_popover (
tags$b("Samtools executable folder"),
"Samtools executable folder",
text[["dp_samtools_exec_dir"]]
),
br(), br(),
shinyDirButton('dp_bam_dir',
'Select folder',
'Please select folder containing the single cell BAM files',
FALSE) %>%
make_title_help_popover (
tags$b("BAMs folder"),
"BAMs folder",
text[["dp_bam_dir"]]
),
br(), br(),
tags$b("Output folder"),
br(), br(),
tags$b("Run"),
br(),
actionButton("dp_exec", "Compute depth"),
br(), br(),
## tags$b("Result"),
## br(),
## verbatimTextOutput("dp_par"),
),
## Variants tab
tabPanel(
"Variants",
br(),
tags$h3("Variant filters"),
br(),
helpText(text[["va_tab_help"]]),
fluidRow(column(4,
br(), br(),
numericInput(
inputId = "va_depth_minimum",
label = "Minimum depth",
min = 0,
max = 500,
step = 1,
value = 3
) %>%
make_shiny_help_popover(
"Minimum depth",
text[["va_depth_minimum"]]
),
br(),
numericInput(
inputId = "va_missing_values_max",
label = "Max missing value",
min = 0.0,
max = 1.0,
step = 0.05,
value = 0.4
) %>%
make_shiny_help_popover(
"Maximumax missing value",
text[["va_missing_values_max"]]
),
br(),
numericInput(
inputId = "va_minumum_median_total", # minimum median depth for total reads
label = "Site minumum median depth:",
min = 0,
max = 500,
step = 1,
value = 8
) %>%
make_shiny_help_popover(
"Minumum median depth per site",
text[["va_minumum_median_total"]]
),
br(),
numericInput(
inputId = "va_minumum_median_mutation", # minimum median depth for reads supporting mutations
label = "Mutation minimum median depth",
min = 0,
max = 500,
step = 1,
value = 4
) %>%
make_shiny_help_popover(
"Minimum median depth per mutation",
text[["va_minumum_median_mutation"]]
),
br(),
br(),
br(),
selectizeInput(
'va_verified_genes',
'Select variant genes',
NULL,
multiple = TRUE,
options = list (
placeholder = 'Choose genes for inferential analysis',
hideSelected = FALSE,
plugins =
list("drag_drop",
"remove_button",
"dropdown_header",
"restore_on_backspace"),
dropdown_header =
list(title = 'a')
)
) %>%
make_shiny_help_popover(
"Variant gene selection",
text[["va_verified_genes"]]
),
),
column(8,
br(),
br(),
#plot
plotOutput('va_filtered_bin_hmap', height = 600)
)
),
br(),
br(),
tags$b("Overview of post-filtered mutations"),
br(),
br(),
DTOutput("va_out"),
br(), br(),
tags$b("Run"),
br(),
actionButton("va_exec", "Select variants"),
br(),
br(),
## tags$b("Result"),
## verbatimTextOutput("va_filters")
),
## Inference tab
tabPanel(
"Inference",
br(),
tags$h3("Longitudinal tree inference parameters"),
br(),
helpText(text[["inf_tab_help"]]),
br(), br(),
numericInput(
inputId = "inf_learning_rate",
label = "Learning rate",
min = 0.01,
max = 10,
step = 0.1,
value = 1
) %>%
make_shiny_help_popover(
"Learning rate",
text[["inf_learning_rate"]]
),
br(),
div(id = "inf_alpha_div",
tagList(
br(),
span() %>%
make_title_help_popover (
tags$b("False positive rates"),
"False positive rate",
text[["inf_alpha"]]
),
span("Insert a set of false positive rates, one \\(\\alpha\\) for each sampling time point. Fill the last row to add further sets of rates to be used in the inference."),
DTOutput('inf_alpha', width = '100%'),
br()
)
),
## br(),
div(id = "inf_beta_div",
tagList(
br(),
span() %>%
make_title_help_popover (
tags$b("False negative rates"),
"False negative rate",
text[["inf_beta"]]
),
span("Insert a set of false negative rates, one \\(\\beta\\) for each sampling time point. Fill the last row to add further sets of rates to be used in the inference."),
DTOutput('inf_beta', width = '100%'),
br()
)
),
br(), br(),
numericInput(
inputId = "inf_num_iter",
label = "Number of iterations",
min = 100,
max = 4000,
step = 100,
value = 10000
) %>%
make_shiny_help_popover(
"Number of iterations",
text[["inf_num_iter"]]
),
br(),
numericInput(
inputId = "inf_num_rs",
label = "Number of restarts",
min = 1,
max = 100,
step = 10,
value = 50
) %>%
make_shiny_help_popover(
"Number of restarts",
text[["inf_num_rs"]]
),
br(),
numericInput(
inputId = "inf_n_try_bs",
label = "Early stopping",
min = 100,
max = 1000,
step = 100,
value = 500
) %>%
make_shiny_help_popover(
"Early stopping",
text[["inf_n_try_bs"]]
),
br(),
numericInput(
inputId = "inf_num_processes",
label = "Number of parallel processes",
min = 1,
max = 100,
step = 5,
value = 10
) %>%
make_shiny_help_popover(
"Number of parallel processes",
text[["inf_num_processes"]]
),
br(),
numericInput(
inputId = "inf_seed",
label = "Seed",
min = 0,
max = NA,
step = 1000,
value = 1121
) %>%
make_shiny_help_popover(
"Seed",
text[["inf_seed"]]
),
br(),
checkboxInput("inf_random_tree",
tags$b("Random tree intialization"),
FALSE) %>%
make_shiny_help_popover(
"Random tree intialization",
text[["inf_random_tree"]]
),
checkboxInput("inf_marginalize",
tags$b("Marginalize"),
FALSE) %>%
make_shiny_help_popover(
"Marginalize",
text[["inf_marginalize"]]
),
checkboxInput("inf_keep_equivalent",
tags$b("Keep equivalent"),
FALSE) %>%
make_shiny_help_popover(
"Keep equivalent",
text[["inf_keep_equivalent"]]
),
checkboxInput("inf_check_indistinguishable",
tags$b("Check indistinguishable"),
FALSE) %>%
make_shiny_help_popover(
"Check indistinguishable",
text[["inf_check_indistinguishable"]]
),
checkboxInput("inf_error_move",
tags$b("Error move"),
FALSE) %>%
make_shiny_help_popover(
"Error move",
text[["inf_error_move"]]
),
checkboxInput("inf_show",
tags$b("Show results in interface")) %>%
make_shiny_help_popover(
"Show results in interface",
text[["inf_show"]]
),
br(), br(),br(),
tags$b("Run"),
br(),
actionButton("inf_next", "Run LACE"),
br(), br(),
tags$b("Result"),
verbatimTextOutput("inf_par")
),
## results ####
tabPanel(
"Longitudinal display",
br(),
inline(actionLink("res_refresh", "Refresh page")),
inline(textOutput("res_lastrefresh")),
br(),
# #widgetframeOutput('LCT_FP', width = "1000px", height = "800px"),
# #LACE:::LACEOutput('LCT_FP'),#, width = 910, height = 800),
# {
# #x <-LACE:::LACEOutput('LCT_FP')
# #htmlwidgets::saveWidget(x,"LACE_result.html")
# NULL
# #x
# },
uiOutput("res"),
br(),br(),
)
)
)
)
)
)
)
### server -- ####
server <- function(input, output, session) {
setwd(.my_pkg_dir) # per non disperdersi
inputs <- list()
inputs[["null_reactiveVal"]] <- reactiveVal("")
observe({
input$null_reactiveVal > 0
}, )
types_ <- reactiveVal()
session$onSessionEnded(function() {
stopApp()
})
## Source?
source("check_demo.R", local = TRUE)
source("load_and_save.R", local = TRUE)
source("project_mgr.R", local = TRUE)
source("pipeline_io_ctrl.R")
source('alpha_beta_table.R', local = TRUE)
source("annotation.R")
source("filters_computation.R", local = TRUE)
source("depth_computation.R", local = TRUE)
source("step3_explore_lace_input_data.R")
source("make_lace_final_input.R")
default_yaml <-
list(".config_06_inf.yml" = list(),
".config_05_va.yml" = list(),
".config_04_dp.yml" = list(),
".config_03_thr.yml" = list(),
".config_02_av.yml" = list(),
".config_01_m.yml" = list()
)
os_hidden <- "."
os_conf <- list()
os_conf[["windows"]] <- "AppData"
os_conf[["mac"]] <- "Library"
os_conf[["unix"]] <- ".config"
os_conf_subdir = "config"
config_path = os_conf_subdir # to remove
## roots_dir=c(root = file.path('..'), "working_dir" = file.path('.'), getVolumes()())
roots_dir = c("project dir" = file.path("."),
".." = file.path(".."),
"../.." = file.path("..",".."),
"../../.." = file.path("..","..",".."),
getVolumes()())
## runjs(jsCode)
## runjs("console.log(shinyBS.addTooltip)")
## js$addTooltip("av_anovar_db_dir", "IL BOTTONE", "")
## addPopover(session, "av_anovar_db_dir", "IL BOTTONE2", "e il polpettone", placement = "right")
observe({
#browser()
if (!is.null(input$close)) {
if (input$close > 0) stopApp() # stop shiny
}
}, )
m_loaded_input_ <- reactiveVal()
av_loaded_input_ <- reactiveVal()
thr_loaded_input_ <- reactiveVal()
dp_loaded_input_ <- reactiveVal()
va_loaded_input_ <- reactiveVal()
inf_loaded_input_ <- reactiveVal()
rs_ <- reactiveVal()
inputs[["res_lastrefresh"]] <- reactiveVal("")
stime <- reactiveVal(2)
port <- reactiveVal()
sopt <- reactiveVal(callr::r_session_options())
av_grep_str= "^av_|^`av_|_av_"
thr_grep_str= "^thr_|^`thr_|_thr_"
dp_grep_str= "^dp_|^`dp_|_dp_"
va_grep_str= "^va_|^`va_|_va_"
inf_grep_str= "^inf_|^`inf_|_inf_"
m_grep_str= "^m_|^`m_|_m_|sc"
inf_uis = c("inf_num_iter",
"inf_num_rs",
"inf_n_try_bs",
"inf_num_processes",
"inf_seed",
"inf_random_tree",
"inf_marginalize",
"inf_keep_equivalent",
"inf_check_indistinguishable",
"inf_show",
"inf_learning_rate",
"inf_error_move")
va_uis= c('va_depth_minimum',
'va_missing_values_max',
'va_minumum_median_total',
'va_minumum_median_mutation')
thr_uis = c('thr_alleles_ratio',
'thr_maf',
'thr_freq',
'thr_accepted_var',
'thr_negleted_var')
dp_uis= c('dp_samtools_exec_dir', 'dp_bam_dir')
av_dir_uis = c('av_anovar_exec_dir',
'av_anovar_db_dir',
'av_vcf_in_dir')
source("project_tab.R", local = TRUE)
source("inference_tab.R", local = TRUE)
setwd(.my_actual_wd)
### Dashboard reactiveVals ####
inputs[["demo"]] <- reactiveVal()
inputs[["reload_project"]] <- reactiveVal()
inputs[["demo_remainder"]] <- reactiveVal()
inputs[["long_job"]] <- reactiveVal(0)
### End dashboard reactiveVals ####
### Dashboard observers ####
shinyjs::hide(id="computation_idCol_div")
observeEvent(inputs[["reload_project"]](), {
proj_dir <- inputs[["reload_project"]]()
if (inputs[["reload_project"]]() != 1 && inputs[["reload_project"]]() != 0)
{
if (dir.exists(proj_dir)) {
#browser()
hide_tab()
inputs[["reload_project"]](1)
inputs[["pr_path"]](proj_dir)
}
else
inputs[["reload_project"]](NULL)
}
#else
# inputs[["reload_project"]](NULL)
})
observeEvent( inputs[["demo"]](),{
if(inputs[["demo"]]() == "Small_dataset" || inputs[["demo"]]() == "Rambow_dataset")
{
#browser()
if(!check_demo()) {
inputs[["demo"]](NULL)
toggle_inputs(is.null(inputs[["demo"]]()))
showNotification("Impossible to download demos.", duration = 10, type = "warning")
}
else
{
#browser()
demo_dir<-file.path(.my_pkg_dir,inputs[["demo"]]())
# create tmp folder
tmp_dir <- tempdir()
tmp_path <- file.path(tmp_dir,inputs[["demo"]]())
dir.create(tmp_path, showWarnings = FALSE)
inputs[["demo_remainder"]](tmp_path)
# fill tmp folder
if (dir.exists(tmp_path) && dir.exists(demo_dir))
{
#delay(100, {
#browser()
hide_tab()
#})
dir_copy(demo_dir, tmp_path, overwrite = TRUE)
inputs[["demo"]](1) # temporary project ready
inputs[["pr_path"]](tmp_path)
}
else
{
#browser()
inputs[["demo"]](NULL)
toggle_inputs(is.null(inputs[["demo"]]()))
}
# disable tab
#shinyjs::addClass()
#shinyjs::disable(selector = '.nav-tabs a[data-value="SC metadata"')
#shinyjs::disable(selector = '.navbar-nav a[data-value="Annotations"')
# load output
}
}
#else
# inputs[["demo"]](NULL)
}, ignoreInit = TRUE)
# observeEvent(input[["sidebarItemExpanded"]], {
# print(input[["sidebarItemExpanded"]])
#
# if(input$sidebarItemExpanded == "projects") {
#
# }
# })
createmenuitem <- function(x, projs) {
#browser()
if (dir.exists(projs[[x]]))
menuSubItem(
text = names(projs)[x],
tabName = str_replace_all(
normalizePath(projs[[x]]),
pattern = .Platform$file.sep,
replacement = ","
)
)
else
NULL
}
observeEvent(input[["sidemenu"]], {
#browser()
projs <- update_proj_list(NULL)
# createmenuitem <- function(x) {
# menuSubItem(
# text = names(projs)[x],
# tabName = str_replace_all(
# normalizePath(projs[[x]]),
# pattern = .Platform$file.sep,
# replacement = ","
# )
# )
# }
submenus <- lapply(seq_along(projs), FUN = function(x) {createmenuitem(x,projs)})
recent_projects <- menuItem("Recent Projects", submenus,
icon = icon("history"))
output$recent_projects <- renderMenu({recent_projects})
log2_print(recent_projects, msg = "LACEview: recent projects =")
}, once = TRUE )
observeEvent( input[["sidemenu"]],{
log2_print(input[["sidemenu"]], msg = "LACEview:")
#browser()
if (input[["sidemenu"]] == "Small dataset") {
inputs[["demo"]]("Small_dataset")
}
if (input[["sidemenu"]] == "Melanoma dataset") {
inputs[["demo"]]("Rambow_dataset")
}
if (input[["sidemenu"]] != "Small dataset" && input[["sidemenu"]] != "Melanoma dataset") {
proj_dir <- str_replace_all(input[["sidemenu"]], pattern = ",", replacement = .Platform$file.sep)
inputs[["reload_project"]](proj_dir)
}
if (input[["sidemenu"]] == "save_tab")
save_tab()
if (input[["sidemenu"]] == "load_tab")
load_tab()
if (input[["sidemenu"]] == "load_tabs")
load_tabs()
if (input[["sidemenu"]] == "quit_app")
stopApp()
if (input[["sidemenu"]] == "new_proj"){
#inputs[["pr_path"]]("")
print("NEW project!!")
inputs[["pr_folder"]]("")
inputs[["pr_folder_std"]](.my_actual_wd)
inputs[["pr_name"]]("")
inputs[["pr_name_std"]]("")
inputs[["project_folder_std"]](.my_actual_wd)
project_folder <- list( "path"="", "root"="")
project_folder$path[[1]]<-""
project_folder$path <-
c(project_folder$path,
as.list(path_split(path_rel(inputs[["project_folder_std"]](),
start = roots_dir[[".."]]))[[1]]))
project_folder$root=".."
inputs[["project_folder"]](project_folder)
updateActionButton(session,"pr_folder", label=inputs[["pr_folder_std"]]())
updateTextInput(session,"pr_name", value=inputs[["pr_name_std"]]())
#inputs[["pr_path"]](.my_actual_wd) #not necessary
}
}, ignoreInit = TRUE)
# observe({
# if (input[["sidemenu"]] == "Small dataset") {
# inputs[["demo"]]("Small dataset")
# }
# if (input[["sidemenu"]] == "Melanoma dataset") {
# inputs[["demo"]]("Melanoma dataset")
# }
# })
save_tab <- function () {
if(!inputs[["project_loaded"]]()) {
showNotification("No porject created or loaded.", duration = 10, type = "warning")
return(NULL)
}
config_path <- file.path(inputs[["project_folder_std"]](), os_conf_subdir)
grep_str <- NULL
#browser()
if (input[["main_tabset"]] == "SC metadata") {
grep_str <- m_grep_str
config_file <- ".config_01_m.yml"
} else if (input[["main_tabset"]] == "Annotations") {
grep_str <- av_grep_str
config_file <- ".config_02_av.yml"
} else if (input[["main_tabset"]] == "Filters") {
grep_str <- thr_grep_str
config_file <- ".config_03_thr.yml"
} else if (input[["main_tabset"]] == "SC sampling depths") {
grep_str <- dp_grep_str
config_file <- ".config_04_dp.yml"
} else if (input[["main_tabset"]] == "Variants") {
grep_str <- va_grep_str
config_file <- ".config_05_va.yml"
} else if (input[["main_tabset"]] == "Inference") {
grep_str <- inf_grep_str
config_file <- ".config_06_inf.yml"
}
if (!is.null(grep_str)) {
doSave(grep_str, config_path, config_file)
showNotification(paste(input[["main_tabset"]], "configuration tab saved"),
duration = 10)
}
updateTabItems(session, "sidemenu", "hidden_menu")
}
load_tab <- function() {
if(!inputs[["project_loaded"]]()) {
showNotification("No porject created or loaded.", duration = 10, type = "warning")
return(NULL)
}
if(input[["main_tabset"]] == "Project")
return(NULL)
config_path <- file.path(inputs[["project_folder_std"]](), os_conf_subdir)
if (input[["main_tabset"]] == "SC metadata") {
m_doLoad_a(config_path)
m_doLoad_b()
} else if (input[["main_tabset"]] == "Annotations") {
av_doLoad_a(config_path)
uis <- av_dir_uis
for (i in av_dir_uis) {
av_doLoad_b(i)
}
} else if (input[["main_tabset"]] == "Filters") {
thr_doLoad_a(config_path)
uis <- thr_uis
for(i in thr_uis) {
thr_doLoad_b(i)
}
} else if (input[["main_tabset"]] == "SC sampling depths") {
dp_doLoad_a(config_path)
uis <- dp_uis
for(i in dp_uis) {
dp_doLoad_b(i)
}
} else if (input[["main_tabset"]] == "Variants") {
va_doLoad_a(config_path) #
uis <- va_uis
for(i in va_uis) {
va_doLoad_b(i)
}
va_doLoad_c()
} else if (input[["main_tabset"]] == "Inference") {
browser()
inf_doLoad_a(config_path)
uis <- inf_uis
for(i in uis) {
inf_doLoad_b(i)
}
inf_doLoad_c()
}
showNotification(paste(input[["main_tabset"]], "configuration tab loaded"), duration = 10)
updateTabItems(session, "sidemenu", "hidden_menu")
}
load_tabs <- function() {
if(!inputs[["project_loaded"]]()) {
showNotification("No porject created or loaded.", duration = 10, type = "warning")
return(NULL)
}
config_path <- file.path(inputs[["project_folder_std"]](), os_conf_subdir)
m_doLoad_a(config_path)
m_doLoad_b()
av_doLoad_a(config_path)
uis <- av_dir_uis
for (i in av_dir_uis) {
av_doLoad_b(i)
}
thr_doLoad_a(config_path)
uis <- thr_uis
for(i in thr_uis) {
thr_doLoad_b(i)
}
dp_doLoad_a(config_path)
uis <- dp_uis
for(i in dp_uis) {
dp_doLoad_b(i)
}
va_doLoad_a(config_path) #
uis <- va_uis
for(i in va_uis) {
va_doLoad_b(i)
}
va_doLoad_c()
browser()
inf_doLoad_a(config_path)
uis <- inf_uis
for(i in uis) {
inf_doLoad_b(i)
}
inf_doLoad_c()
showNotification(paste("project", "configuration reset to saved state"), duration = 10)
updateTabItems(session, "sidemenu", "hidden_menu")
}
catch_ui_files_priority = 1
observe({
save_ui_state(m_grep_str, "config_01_m.yml")
save_ui_state(av_grep_str, "config_02_av.yml")
save_ui_state(thr_grep_str, "config_03_thr.yml")
save_ui_state(dp_grep_str, "config_04_dp.yml")
save_ui_state(va_grep_str, "config_05_va.yml")
save_ui_state(inf_grep_str, "config_06_inf.yml")
},
priority = catch_ui_files_priority)
### End dashboard observers ####
update_proj_list <- function (project_folder) {
#browser()
os_conf_tmp <- file.path(path_home(), os_conf[[.Platform$OS.type]], "LACE")
if(dir.exists(os_conf_tmp)) {
if(file.exists(file.path(os_conf_tmp, "projects_list.yml")))
projects_list <- read.config(file = file.path(os_conf_tmp, "projects_list.yml"))
else
projects_list <- list()
}
else
projects_list <- list()
if(!is.list(projects_list))
projects_list <- list()
mask <- (projects_list %in% project_folder)
if (length(which(mask))>0) {
projects_list <- projects_list[-which(mask)]
}
if (!is.null(project_folder))
projects_list <- c(list(project_folder), projects_list)
names(projects_list) <- lapply(
seq_along(projects_list),
FUN = function(x) {
basename(projects_list[[x]])
})
write.config(config.dat = projects_list,
file.path = file.path(os_conf_tmp, "projects_list.yml"),
write.type = "yaml")
return(projects_list)
}
### Dashboard outputs ####
### End dashboard outputs ####
### Variational reactiveVals ####
va_uis <- c('va_depth_minimum',
'va_missing_values_max',
'va_minumum_median_total',
'va_minumum_median_mutation')
for (va_ui in va_uis)
inputs[[va_ui]] <- reactiveVal()
## inputs[['va_data_in_dir']] <- reactive(inputs[['thr_out_dir']]())
## dir <- out_subfolder_compute(inputs[['project_folder']](), 'filtered_var')
## inputs[['va_out_dir']] <- reactive(dir)
inputs[['va_verified_genes']] <- reactiveVal()
inputs[['va_list_genes']] <- reactiveVal()
## va_data_in_dir_ <- reactive(parseDirPath(roots=roots_dir, inputs[['va_data_in_dir']]()))
va_depth_minimum_ <-
reactive(inputs[['va_depth_minimum']]())
va_missing_values_max_ <-
reactive(inputs[['va_missing_values_max']]())
va_minumum_median_total_ <-
reactive(inputs[['va_minumum_median_total']]())
va_minumum_median_mutation_ <-
reactive(inputs[['va_minumum_median_mutation']]())
va_out_dir_ <-
reactive(parseDirPath(roots=roots_dir, inputs[['va_out_dir']]()))
va_non_NA_genes_ <- reactiveVal(NULL)
va_compute_output_ <- reactiveVal(NULL)
files_ <- reactiveVal(NULL)
list_genes_ <-
reactive(inputs[['va_list_genes']]())
verified_genes_ <-
reactive(inputs[['va_verified_genes']]())
va_rvs = reactiveValues(va_buttons = list(), va_observers = list())
### End variational reactiveVals ####
### Variational functions ####
va_exec <- function () {
#browser()
if (length(va_out_dir_()) == 0)
return()
if (!is.integer(inputs[['thr_out_dir']]()) &&
!is.integer(inputs[['dp_out_dir']]())) {
if (dir.exists(thr_out_dir_()) &&
dir.exists(dp_out_dir_())) {
#browser()
valid_genes_names <-
NA_compute(va_depth_minimum_(),
va_missing_values_max_(),
thr_out_dir_(),
dp_out_dir_(),
va_out_dir_(),
inputs[['m_time_points']]())
va_non_NA_genes_(valid_genes_names)
#browser()
files <- NA_compute2_load(thr_out_dir_(),
dp_out_dir_(),
va_out_dir_())
files_(files)
} else
showNotification(paste("Annotated VCF folder does not exist"),
duration = 10,
type = "warning")
} else
showNotification(paste("Annotated VCF folder is not set"),
duration = 10,
type = "warning")
}
va_exec2 <- function() {
req(inputs[['thr_out_dir']](), inputs[['dp_out_dir']]())
if (!is.integer(inputs[['thr_out_dir']]()) &&
!is.integer(inputs[['dp_out_dir']]()))
if (dir.exists(thr_out_dir_()) &&
dir.exists(dp_out_dir_()))
if (any(!sapply(files_(), is.null))){ # files not found
#browser()
NA_c2 <-
NA_compute2(va_depth_minimum_(),
va_minumum_median_total_(),
va_minumum_median_mutation_(),
thr_out_dir_(),
dp_out_dir_(),
va_out_dir_(),
inputs[['m_time_points']](),
verified_genes_(),
va_non_NA_genes_(),
files_())
#browser()
va_compute_output_(NA_c2$distinct_mutations)
#ggsave(file=file.path(inputs[["project_folder_std"]](),"D.svg"), plot=NA_c2$g, width=10, height=10)
output$va_filtered_bin_hmap <- renderPlot({
NA_c2$g
}, height = 600)
} else {
if (!is.null(files_()))
showNotification(paste("Files from previous steps not computed"),
duration = 10,
type = "warning")
} else
showNotification(paste("Sampling depth folder does not exist"),
duration = 10,
type = "warning")
else
showNotification(paste("Sampling depth folder is not set"),
duration = 10,
type = "warning")
}
### End variational functions ####
### Variational observers ####
observe({
va_rvs$observers =
lapply(va_uis,
function(i) {
observe({
req(inputs[[i]]())
})
}
)
},
priority = -1)
observeEvent(reactiveValuesToList(input), {
outs <- outputOptions(output)
lapply(names(outs),
function(name) {
outputOptions(output,
name,
suspendWhenHidden = FALSE)
})
},
once = TRUE,
priority = -1)
observe({
va_observers = lapply(va_uis,
function(i) {
observeEvent(input[[i]], {
## req(input)
inputs[[i]](input[[i]])
})
output[[i]] <- renderText(inputs[[i]]())
})
},
priority = -1)
observeEvent(inputs[['av_anovar_db_dir']](), {
#browser()
req(inputs[['av_anovar_db_dir']]())
## req(inputs[['thr_out_dir']](), inputs[['dp_out_dir']]())
## if (!is.integer(inputs[['thr_out_dir']]()) && !is.integer(inputs[['dp_out_dir']]())) {
if (!is.integer(inputs[['av_anovar_db_dir']]())) {
## if (dir.exists(thr_out_dir_()) && dir.exists(dp_out_dir_())) {
if (dir.exists(av_anovar_db_dir_())) {
## if (file.exists(file.path( thr_out_dir_(), "snpMut_filt_freq.rds"))){
fa_file <-
file_path_sans_ext(list.files(path = av_anovar_db_dir_(),
pattern = ".*.fa")[1])
ref_files <-
list.files(path = av_anovar_db_dir_(),
pattern = ".*.[^f][^a]")
ref_files2 <-
file_path_sans_ext(ref_files)
ref_files2 <-
ref_files[str_detect(fa_file, ref_files2)]
ref_files2 <-
ref_files2[which.min(str_length(ref_files2))]
ref_files2 <-
file.path(av_anovar_db_dir_(), ref_files2)
if (length(file.exists(ref_files2))>0) {
if (file.exists(ref_files2)) {
ref_info <-
read.table(file = ref_files2,
header = FALSE,
sep = '\t',
stringsAsFactors = FALSE)
list_gene_symbols <- ref_info[, 13]
## if (file.exists(file.path( av_anovar_db_dir_(), "snpMut_filt_freq.rds"))){
## print('LOAD FILE2')
## snpMut_filt_freq <- readRDS(file=paste0(file.path( thr_out_dir_(), "snpMut_filt_freq.rds")))
## print(head(snpMut_filt_freq))
} else {
showNotification(paste("annovar reference file",
ref_files2,
"not found"),
duration = 10,
type = "warning")
}
}
#not necessary
if (file.exists(file.path( va_out_dir_(), "snpMut_filt_freq_reduced.rds"))) {
snpMut_filt_freq <- readRDS(file=paste0(file.path( va_out_dir_(), "snpMut_filt_freq_reduced.rds")))
inputs[['va_list_genes']](sort(unique(snpMut_filt_freq$Gene)))
} else
inputs[['va_list_genes']](list_gene_symbols)
updateSelectizeInput(session,
'va_verified_genes',
choices = inputs[['va_list_genes']](),
selected = inputs[['va_verified_genes']](),
server = TRUE)
}
}
})
observeEvent(input[['va_verified_genes']], {
#req(input[['va_verified_genes']])
#browser()
inputs[['va_verified_genes']](input[['va_verified_genes']])
}, ignoreNULL = FALSE)
va_iv <- InputValidator$new()
va_iv$add_rule("va_depth_minimum", sv_between(0,500))
va_iv$add_rule("va_missing_values_max", sv_between(0.,1.))
va_iv$add_rule("va_minumum_median_total", sv_between(0,500))
va_iv$add_rule("va_minumum_median_mutation", sv_between(0,500))
va_iv$enable()
observeEvent(input$va_exec,{
req(va_iv$is_valid())
#browser()
va_exec()
if (file.exists(file.path( va_out_dir_(), "snpMut_filt_freq_reduced.rds"))) {
snpMut_filt_freq <- readRDS(file=paste0(file.path( va_out_dir_(), "snpMut_filt_freq_reduced.rds")))
inputs[['va_list_genes']](sort(unique(snpMut_filt_freq$Gene)))
}
updateSelectizeInput(session,
'va_verified_genes',
choices = inputs[['va_list_genes']](),
selected = inputs[['va_verified_genes']](),
server = TRUE)
va_exec2()
#browser()
#print("a")
})
observeEvent({ c(#files_(),
va_depth_minimum_(),
va_missing_values_max_(),
va_minumum_median_total_(),
va_minumum_median_mutation_(),
verified_genes_()
)
},
{
va_exec()
va_exec2()
},
ignoreNULL = FALSE,
ignoreInit = TRUE)
### End Variational observers ####
### Variational outputs ####
output$va_out <-
DT::renderDT(va_compute_output_(), server = TRUE)
#output[['va_verified_genes']] <-
# renderText(inputs[['va_verified_genes']]())
#output[['va_list_genes']] <-
# renderPrint(inputs[['va_list_genes']]())
#output[['va_out_dir']] <-
# renderText(parseDirPath(roots = roots_dir,
# inputs[['va_out_dir']]()))
output[['va_filters']] <-
renderPrint({
list(va_data_in_dir = parseDirPath(roots=roots_dir,
inputs[['thr_out_dir']]()),
depth_minimum = inputs$va_depth_minimum(),
missing_values_max = inputs$va_missing_values_max(),
minumum_median_total = inputs$va_minumum_median_total(),
minumum_median_mutation = inputs$va_minumum_median_mutation(),
va_out_dir = parseDirPath(roots = roots_dir,
inputs[['va_out_dir']]()),
va_verified_genes = inputs[['va_verified_genes']]())
})
### End variational outputs ####
### Depth reactivaVals ####
dp_uis <- c('dp_samtools_exec_dir', 'dp_bam_dir')
dp_rvs = reactiveValues(dp_buttons = list(), dp_observers = list())
###
for (dir_ui in dp_uis) {
defaultPath <- ""
# if(dir_ui == "dp_samtools_exec_dir")
# defaultPath <- path_rel(dirname(Sys.which("samtools")), start = "..")
shinyDirChoose(input,
dir_ui,
roots = roots_dir,
filetypes = c('', 'txt'),
defaultPath = defaultPath,
defaultRoot = "..")
}
for (dp_ui in dp_uis)
inputs[[dp_ui]] <- reactiveVal()
inputs[['dp_mut_dir']] <-
reactive(inputs[['thr_out_dir']]())
## inputs[['dp_out_dir']] <- reactiveVal()
dp_samtools_exec_dir_ <-
reactive(parseDirPath(roots = roots_dir,
inputs[['dp_samtools_exec_dir']]()))
dp_samtools_ <-
reactive(file.path(dp_samtools_exec_dir_(),
'samtools'))
dp_bam_dir_ <-
reactive(parseDirPath(roots = roots_dir,
inputs[['dp_bam_dir']]()))
dp_out_dir_ <-
reactive(parseDirPath(roots = roots_dir,
inputs[['dp_out_dir']]()))
dp_mut_dir_ <-
reactive(parseDirPath(roots = roots_dir,
inputs[['dp_mut_dir']]()))
### End depth reactivaVals ####
### Depth observers ####
observe({
dp_rvs$observers =
lapply(dp_uis,
function(i) {
observe({
req(inputs[[i]]())
updateActionButton(session, i, label = set_dir_ui(i))
})
}
)
},
priority = -1)
observeEvent(reactiveValuesToList(input), {
outs <- outputOptions(output)
lapply(names(outs),
function(name) {
outputOptions(output,
name,
suspendWhenHidden = FALSE)
})
},
once = TRUE,
priority = -1)
## observeEvent(reactiveValuesToList(input),{
## lapply(dp_uis, function(i) {
## click(i)
## hide(paste0(i,'-modal'))
## delay(300,runjs(paste0("$('#",i,"-modal #sF-cancelButton').click()")))
## })
## },once = T, priority = -1)
observe({
dp_observers = lapply(dp_uis,
function(i) {
observeEvent(input[[i]], {
req(input)
inputs[[i]](input[[i]])
})
output[[i]] <-
renderText(parseDirPath(roots = roots_dir,
inputs[[i]]()))
}
)},
priority = -1)
observeEvent(dp_samtools_exec_dir_(), {
if (!is.integer(input[['dp_samtools_exec_dir']])) {
if (file.exists(dp_samtools_()))
showNotification(paste("found samtools"),
duration = 10,
type = "message")
else
showNotification(paste("samtools", 'not present in',
dp_samtools_exec_dir_()),
duration = 10,
type = "warning")
}
})
### End depth observers ####
### Depth functions ####
dp_exec <- function() {
if (length(dp_out_dir_()) == 0)
return()
Opt = list() # MA: Perche` maiuscolo il nome della variabile?
Opt$StoredFile <- file.path(config_path, ".config_04_dp.yml")
Opt$ActFile <- file.path(config_path, "config_04_dp.yml")
Opt$ExtraFiles = NULL
OutFiles <- c("final_data_depth.txt", "final_data_mut.txt")
chk_files <- ManyInSomeOut(dp_bam_dir_(),
InFilesMask = ".*.bam$",
OutDir=dp_out_dir_(),
OutFiles = OutFiles,
Opt = Opt)
InFilesToDo <- chk_files$InFilesToDo
## Use metadata if available
if (!is.integer(inputs[['sc_metadata_file']]())) {
if (file.exists(sc_metadata_label_())) {
if (inputs[['m_id_column']]() %in% colnames(sc_metadata_()))
InFilesToDo <-
InFilesToDo[str_split_fixed(InFilesToDo,
"\\.",
n = 2)[, 1] %in%
as.character(sc_metadata_()[[inputs[['m_id_column']]()]])]
else
showNotification(paste("no valid metadata id column"),
duration = 10,
type = "warning")
} else
showNotification(paste("no valid metadata file"), duration = 10, type = "warning")
} else
showNotification(paste("no valid metadata file"), duration = 10, type = "warning")
InFilesToDo <-
file.path(dp_bam_dir_(), chk_files$InFilesToDo)
OutFilesToRm <-
file.path(dp_out_dir_(), chk_files$OutFilesToRm)
if (!is.integer(inputs[['dp_samtools_exec_dir']]()) &
!is.integer(inputs[['dp_bam_dir']]()) &
!is.integer(inputs[['dp_mut_dir']]())) {
if (dir.exists(dp_samtools_exec_dir_()) &
file.exists(dp_samtools_()) &
dir.exists(dp_bam_dir_()) & dir.exists(dp_mut_dir_())) {
dp_compute(sc_metadata_(),
dp_bam_dir_(),
dp_samtools_(),
thr_out_dir_(),
dp_out_dir_(),
inputs[['m_id_column']](),
InFilesToDo,
OutFilesToRm)
## return(read_file(file.path(dp_out_dir_(), 'stdout.log')))
} else
showNotification(paste("one of the folders or executable does not exist"),
duration = 10,
type = "warning")
} else
showNotification(paste("one of the folders is not set"),
duration = 10,
type = "warning")
return("possible errors")
}
### End depth functions ####
### Depth outputs ####
output$dp_out <- eventReactive(input$dp_exec,{
dp_exec()
})
output[['dp_mut_dir']] <-
renderText(parseDirPath(roots = roots_dir,
inputs[['dp_mut_dir']]()))
output[['dp_par']] <-
renderPrint({
list(samtools =parseDirPath(roots = roots_dir,
inputs$dp_samtools_exec_dir()),
bam_dir = parseDirPath(roots = roots_dir,
inputs$dp_bam_dir()),
mut_dir = parseDirPath(roots = roots_dir,
inputs$dp_mut_dir()),
out_dir = parseDirPath(roots = roots_dir,
inputs$dp_out_dir())
)
})
### End depth outputs ####
### Threshold reactiveVals ####
thr_uis = c('thr_alleles_ratio',
'thr_maf',
'thr_freq',
'thr_accepted_var',
'thr_negleted_var')
###
thr_rvs = reactiveValues(thr_buttons = list(),
thr_observers = list())
for (thr_ui in thr_uis)
inputs[[thr_ui]] <- reactiveVal()
thr_alleles_ratio_ <-
reactive(inputs[['thr_alleles_ratio']]())
thr_maf_ <-
reactive(inputs[['thr_maf']]())
thr_freq_ <-
reactive(inputs[['thr_freq']]())
thr_out_dir_ <-
reactive(parseDirPath(roots = roots_dir,
inputs[['thr_out_dir']]()))
thr_vcf_in_dir_ <-
reactive(parseDirPath(roots = roots_dir,
inputs[['thr_vcf_in_dir']]()))
exonic_list <- list("frameshift insertion",
"frameshift deletion",
"frameshift block substitution",
"stopgain",
"stoploss",
"nonframeshift insertion",
"nonframeshift deletion",
"nonframeshift block substitution",
"nonsynonymous SNV",
"synonymous SNV",
"unknown")
### End threshold reactiveVals ####
### Threshold functions ####
thr_exec <- function() {
if (length(thr_out_dir_()) == 0)
return()
Opt = list()
Opt$StoredFile <- file.path(config_path, ".config_03_thr.yml")
Opt$ActFile <- file.path(config_path, "config_03_thr.yml")
Opt$ExtraFiles = NULL
## chk_files <- OneInOneOut( thr_vcf_in_dir_(), InFilesMask = ".*.exonic_variant_function$", thr_out_dir_(), OutExt = "anninput", Opt = Opt)
OutFiles <- c("cells_aggregate_info.rds",
"scMutInfo.rds",
"SNPInfo.rds",
"snpMut_filt_freq.rds"
)
chk_files <- ManyInSomeOut(thr_vcf_in_dir_(),
InFilesMask =
".*.exonic_variant_function$",
OutDir=thr_out_dir_(),
OutFiles = OutFiles,
Opt = Opt)
InFilesToDo <- chk_files$InFilesToDo
## use metadata if available
if (!is.integer(inputs[['sc_metadata_file']]())) {
if (file.exists(sc_metadata_label_())){
if (inputs[['m_id_column']]() %in% colnames(sc_metadata_()))
InFilesToDo <-
InFilesToDo[str_split_fixed(InFilesToDo,
"\\.",
n = 2)[, 1] %in%
as.character(sc_metadata_()[[inputs[['m_id_column']]()]])]
else
showNotification(paste("no valid metadata id column"),
duration = 10,
type = "warning")
} else
showNotification(paste("no valid metadata file"),
duration = 10,
type = "warning")
} else
showNotification(paste("no valid metadata file"),
duration = 10,
type = "warning")
InFilesToDo <-
file.path(thr_vcf_in_dir_(),
chk_files$InFilesToDo)
OutFilesToRm <-
file.path(thr_out_dir_(),
chk_files$OutFilesToRm)
if (!is.integer(inputs[['thr_vcf_in_dir']]())) {
if (dir.exists(thr_vcf_in_dir_())) {
## filter1_compute(thr_vcf_in_dir_(), sc_metadata_(), thr_alleles_ratio_(), thr_maf_(), thr_freq_(), thr_out_dir_(), m_id_column_(), m_time_column_())
filter1_compute(thr_vcf_in_dir_(),
sc_metadata_(),
thr_alleles_ratio_(),
thr_maf_(),
thr_freq_(),
thr_out_dir_(),
inputs[['m_id_column']](),
inputs[['m_time_column']](),
inputs[['thr_accepted_var']](),
InFilesToDo,
OutFilesToRm)
filter2_compute(thr_vcf_in_dir_(),
sc_metadata_(),
thr_alleles_ratio_(),
thr_maf_(),
thr_freq_(),
thr_out_dir_(),
m_id_column_(),
m_time_column_(),
InFilesToDo,
OutFilesToRm)
snpMut_filt_freq <- filter3_compute(
thr_vcf_in_dir_(),
sc_metadata_(),
thr_alleles_ratio_(),
thr_maf_(),
thr_freq_(),
thr_out_dir_(),
m_id_column_(),
m_time_column_(),
inputs[['m_time_points']](),
InFilesToDo,
OutFilesToRm)
inputs[['va_list_genes']](sort(unique(snpMut_filt_freq$Gene)))
updateSelectizeInput(session,
'va_verified_genes',
choices = inputs[['va_list_genes']](),
selected = inputs[['va_verified_genes']](),
server = TRUE)
return(read_file(file.path(thr_vcf_in_dir_(),
'stdout.log')))
} else
showNotification(paste("Filtered VCF folder does not exist"),
duration = 10,
type = "warning")
} else
showNotification(paste("Filtered VCF folder is not set"),
duration = 10,
type = "warning")
return("Possible errors") # MA: return or raise an error?
}
### End threshold functions ####
### Threshold observers ####
observe({
thr_rvs$observers = lapply(thr_uis,
function(i) {
observe({
req(inputs[[i]]())
## updateActionButton(session, i, label = set_dir_ui(i))
updateNumericInput(session, i, value = inputs[[i]]())
})
}
)
},
priority = -1)
observeEvent(reactiveValuesToList(input), {
outs <- outputOptions(output)
lapply(names(outs),
function(name) {
outputOptions(output,
name,
suspendWhenHidden = FALSE)
})
},
once = TRUE,
priority = -1)
## # observeEvent(reactiveValuesToList(input),{
## # lapply(thr_uis, function(i) {
## # click(i)
## # hide(paste0(i,'-modal'))
## # delay(300,runjs(paste0("$('#",i,"-modal #sF-cancelButton').click()")))
## # })
## # },once = T, priority = -1)
###
## #dir <- out_subfolder_compute(inputs[['project_folder']](),'filtered_vcf')
## #inputs[['thr_out_dir']] <- reactive(dir)
observe({
thr_observers = lapply(thr_uis,
function(i) {
observeEvent(input[[i]], {
req(input)
inputs[[i]](input[[i]])
})
output[[i]] <- renderPrint(inputs[[i]]())
}
)
},
priority = -1)
## Exonic ui
observeEvent(reactiveValuesToList(input), {
inputs[['thr_accepted_var']](exonic_list)
inputs[['thr_negleted_var']](NULL)
},
once = TRUE,
priority = -1)
#observeEvent(input[['thr_accepted_var']],
# {
#browser()
#print(input[['thr_accepted_var']])
#print(inputs[['thr_accepted_var']]())
# })
#observeEvent(inputs[['thr_accepted_var']](),
# {
#browser()
#print(input[['thr_accepted_var']])
#print(inputs[['thr_accepted_var']]())
# })
output$thr_bucket_var_list <-
renderUI({
## showNotification(paste("renderUI[['thr_bucket_var_list']]"), duration = NULL)
bucket_list_basic <-
bucket_list(
header = "Choose the variant functions for inferential analysis",
add_rank_list(
text = "Considered exonic variants",
labels = inputs[['thr_accepted_var']](),
input_id = "thr_accepted_var",
options = sortable_options(multiDrag = TRUE, disabled = !is.null(inputs[["demo"]]()))
),
add_rank_list(
text = "Neglected exonic variants",
labels = inputs[['thr_negleted_var']](),
input_id = "thr_negleted_var",
options = sortable_options(multiDrag = TRUE, disabled = !is.null(inputs[["demo"]]()))
),
group_name = "thr_bucket_var_list",
orientation = "horizontal",
options = sortable_options(disabled = !is.null(inputs[["demo"]]()))
)
x <-
tagList(
span() %>%
make_title_help_popover (
tags$b("Exonic variant function annotations"),
"List of exonic varian functions",
text[["thr_bucket_var_list"]],
server = TRUE
),
bucket_list_basic
)
if (loading_()) {
loaded_(TRUE)
}
x
})
thr_iv <- InputValidator$new()
thr_iv$add_rule("thr_alleles_ratio", sv_between(1,55))
thr_iv$add_rule("thr_maf", sv_between(0.01,0.5))
thr_iv$add_rule("thr_freq", sv_between(0.,1.))
thr_iv$enable()
### Threshold observers ####
### Threshold outputs ####
output[['thr_vcf_in_dir']] <-
renderText(parseDirPath(roots = roots_dir,
inputs[['thr_vcf_in_dir']]()))
output[['thr_out_dir']] <-
renderText(parseDirPath(roots = roots_dir,
inputs[['thr_out_dir']]()))
output[['thr_filters']] <-
renderPrint({
list(thr_vcf_in_dir = parseDirPath(roots = roots_dir,
inputs[['thr_vcf_in_dir']]()),
alleles_ratio = inputs$thr_alleles_ratio(),
maf = inputs$thr_maf(),
freq = inputs$thr_freq(),
thr_out_dir = parseDirPath(roots = roots_dir,
inputs[['thr_out_dir']]()) )
})
output$thr_out <- eventReactive(input$thr_exec, {
req(thr_iv$is_valid())
thr_exec()
})
### End threshold outputs ####
### Annotation reactiveVals ####
av_dir_uis= c('av_anovar_exec_dir',
'av_anovar_db_dir',
'av_vcf_in_dir')
for (dir_ui in av_dir_uis)
inputs[[dir_ui]] <- reactiveVal()
av_rvs = reactiveValues(av_buttons = list(), av_observers = list())
## #dir <- out_subfolder_compute(inputs[['project_folder']](),'vcf_out')
## #inputs[['av_vcf_out_dir']] <- reactive(dir)
av_anovar_exec_dir_ <-
reactive(parseDirPath(roots = roots_dir,
inputs[['av_anovar_exec_dir']]()))
av_anovar_convert_ <-
reactive(file.path(av_anovar_exec_dir_(),
'convert2annovar.pl'))
av_anovar_db_dir_ <-
reactive(parseDirPath(roots = roots_dir,
inputs[['av_anovar_db_dir']]()))
av_vcf_in_dir_ <-
reactive(parseDirPath(roots = roots_dir,
inputs[['av_vcf_in_dir']]()))
av_vcf_out_dir_ <-
reactive(parseDirPath(roots = roots_dir,
inputs[['av_vcf_out_dir']]()))
av_anovar_annot_ <-
reactive(file.path(av_anovar_exec_dir_(),
'annotate_variation.pl'))
### End annotation reactiveVals ####
### Annotation functions ####
set_dir_ui <- function(dir_id,
default_dir_label = 'Select folder',
input_var = inputs,
basedir = "..") { # replace with roots_dir
this_label <- default_dir_label
meta <- input_var[[dir_id]]()
## if (basedir %in% names(meta))
if (!is.null(meta))
if (!is.integer(meta))
if (dir.exists(parseDirPath(roots = roots_dir, meta)))
this_label <- parseDirPath(roots = roots_dir, meta)
return(this_label)
}
out_subfolder_compute <- function(out_dir_inp, sub_dir) {
if ('path' %in% names(out_dir_inp)) {
tmp <- out_dir_inp[['path']]
## tmp <- tmp[-length(tmp)]
out_dir_inp[['path']] <- c(tmp, sub_dir)
}
return (out_dir_inp)
}
av_exec <- function() {
if(length(av_vcf_out_dir_())==0)
return()
log2_print('av_exec', msg = "LACEview:")
log2_print(paste("av_vcf_out_dir_()", av_vcf_out_dir_()), msg = "LACEview:")
Opt = list()
Opt$StoredFile <- file.path(config_path,".config_02_av.yml")
Opt$ActFile <- file.path(config_path,"config_02_av.yml")
Opt$ExtraFiles = NULL
chk_files <- OneInOneOut(av_vcf_in_dir_(),
InFilesMask = ".*vcf$",
av_vcf_out_dir_(),
OutExt =
"anninput.exonic_variant_function",
Opt = Opt)
InFilesToDo <- chk_files$InFilesToDo
## Use metadata if available
if (!is.integer(inputs[['sc_metadata_file']]())) {
if (file.exists(sc_metadata_label_())){
if (inputs[['m_id_column']]() %in% colnames(sc_metadata_()))
InFilesToDo <-
InFilesToDo[str_split_fixed(InFilesToDo,
"\\.",
n = 2)[, 1] %in%
as.character(sc_metadata_()[[inputs[['m_id_column']]()]])]
else
showNotification(paste("no valid metadata id column"),
duration = 10,
type = "warning")
}
else
showNotification(paste("no valid metadata file"),
duration = 10,
type = "warning")
}
else
showNotification(paste("no valid metadata file"),
duration = 10,
type = "warning")
InFilesToDo <- file.path(av_vcf_in_dir_(),
chk_files$InFilesToDo)
OutFilesToRm <- file.path(av_vcf_out_dir_(),
chk_files$OutFilesToRm)
if (!is.integer(inputs[['av_anovar_exec_dir']]()) &
!is.integer(inputs[['av_anovar_db_dir']]()) &
!is.integer(inputs[['av_vcf_in_dir']]())
) {
if (dir.exists(av_anovar_exec_dir_()) &
file.exists(av_anovar_convert_()) &
file.exists(av_anovar_annot_()) &
dir.exists(av_anovar_db_dir_()) &
dir.exists(av_vcf_in_dir_())
) {
av_compute(av_anovar_convert_(),
av_anovar_annot_(),
av_anovar_db_dir_(),
av_vcf_in_dir_(),
av_vcf_out_dir_(),
InFilesToDo = InFilesToDo,
OutFilesToRm = OutFilesToRm)
return(read_file(file.path(av_vcf_out_dir_(),
'stdout.log')))
} else
showNotification(paste("one of the folders or executable does not exist"),
duration = 10,
type = "warning")
} else
showNotification(paste("one of the folders is not set"),
duration = 10,
type = "warning")
return("possible errors") # MA: CHECK THESE!!!! IS THE CHECK!!!
}
### End annotation functions ####
### Annotation observers ####
for (dir_ui in av_dir_uis) { #av_rvs$buttons???
defaultPath <- ""
# if(dir_ui == "av_anovar_exec_dir")
# defaultPath <- path_rel(Sys.which("annotate_variation.pl"), start = "..")
shinyDirChoose(input,
dir_ui,
roots = roots_dir,
defaultPath = defaultPath,
filetypes = c('', 'txt'),
defaultRoot = "..")
}
## Update buttons
observe({
av_rvs$observers = lapply(av_dir_uis,
function(i) {
observe({
req(inputs[[i]]())
updateActionButton(session,
i,
label = set_dir_ui(i))
})
}
)
## reactiveValuesToList(av_rvs)
},
priority = -1)
## Make ui updatable
observeEvent(reactiveValuesToList(input), {
outs <- outputOptions(output)
lapply(names(outs),
function(name) {
outputOptions(output,
name,
suspendWhenHidden = FALSE)
})
},
once = TRUE,
priority = -1)
## observeEvent(reactiveValuesToList(input), {
## lapply(av_dir_uis,
## function(i) {
## click(i)
## hide(paste0(i, '-modal'))
## delay(300,
## runjs(paste0("$('#",
## i,
## "-modal #sF-cancelButton').click()")))
## })
## #delay(1000, runjs("$('.sF-modal modal-dialog modal-lg').keydown(new KeyboardEvent('keydown', {'keyCode': 40}))"))
## #delay(1000,"$('#av_anovar_exec_dir-modal').dispatchEvent(new KeyboardEvent('keydown', {'keyCode': 40}))")
## #delay(1000,runjs("handleArrowKey('down')"))
## },
## once = T,
## priority = -1)
observe({
av_observers = lapply(av_dir_uis,
function(i) {
observeEvent(input[[i]], {
req(input)
inputs[[i]](input[[i]])
})
output[[i]] <-
renderText(parseDirPath(roots = roots_dir,
inputs[[i]]()))
}
)
## reactiveValuesToList(av_rvs)
},
priority = -1)
## observeEvent(inputs[['av_anovar_exec_dir']](),{
observeEvent(av_anovar_exec_dir_(), {
if (!is.integer(input[['av_anovar_exec_dir']])) {
if (file.exists(av_anovar_convert_()))
showNotification(paste("found convert2annovar.pl"),
duration = 10,
type = "message")
else
showNotification(paste("convert2annovar.pl",
'not present in',
av_anovar_exec_dir_()),
duration = 10,
type = "warning")
if (file.exists(av_anovar_annot_()))
showNotification(paste("found annotate_variation.pl"),
duration = 10,
type = "message")
else
showNotification(paste("annotate_variation.pl",'not present in',
av_anovar_exec_dir_()),
duration = 10,
type = "warning")
}
})
output$av_out <- eventReactive(input$av_exec, {
av_exec()
},
ignoreInit = TRUE)
### End annotation observers ####
### Annotation outputs ####
output[['av_vcf_out_dir']] <-
renderText(parseDirPath(roots = roots_dir,
inputs[['av_vcf_out_dir']]()))
output$av_anovar_convert <-
renderText(av_anovar_convert_())
output$av_anovar_annot <-
renderText(av_anovar_annot_())
### End annotation outputs ####
### Metadata reactiveVals ####
loaded_input_ <- reactiveVal(list())
loaded_ <- reactiveVal(FALSE)
m_widgetId_ <- reactiveVal()
loaded_input <- list()
initialInputs <- list()
initialInputs_copy <- list()
the_files <- list()
### End metadata reactiveVals ####
### Metadata observers ####
## add types to ui #remove
observeEvent(input, {
initialInputs <<- reactiveValuesToList(input) # MA: WTF! Ma decidersi sugli assegnamenti????
for (inp in names(initialInputs)) {
## print(inp)
runjs(getWidgetType(inp))
## print(input$inputType)
}
},
once = TRUE,
priority = 5)
## Get types #remove
observe({
types <- list()
for (inp in names(initialInputs))
types[[inp]]<-input[[paste0('inputType_',inp)]]
types_(types)
},
priority = 4)
#####
#####
## widgetId output
observe({
reactiveValuesToList(input)
types<-types_()
for (n in names(initialInputs_copy)) {
if (n %in% names(types))
if (types[[n]] == 'shinyFiles')
if (n %in% names(the_files)) {
## initialInputs_copy[[n]] <<- the_files[[n]]
}
}
m_widgetId_(initialInputs_copy)
},
priority = catch_ui_files_priority - 1)
output$m_widgetId <- renderPrint({
m_widgetId_()
})
shinyFileChoose(input,
'sc_metadata_file',
roots = roots_dir,
filetypes = c('rds',''),
defaultRoot = "..")
## Set_ui_files
set_file_ui <- function(dir_id,
default_dir_label = 'Select file',
input_var = inputs,
basedir = "..") { #replace with roots_dir
this_label <- default_dir_label
meta <- input_var[[dir_id]]()
## if (basedir %in% names(meta))
if (!is.null(meta))
if (!is.integer(meta))
if (file.exists(as.character(parseFilePaths(roots = roots_dir,
meta)[['datapath']])))
this_label <- as.character(parseFilePaths(roots = roots_dir,
meta)[['datapath']])
## showNotification(this_label, duration = 10)
return(this_label)
}
## # output$m_sc_metadata_col <- reactive({
## # if (length(sc_metadata_())>0) {
## # sc_metadata_col <- colnames(sc_metadata_())
## # } else {
## # sc_metadata_col <- c("")
## # }
## # sc_metadata_col
## # })
#####
m_dir_uis = c('sc_metadata_file',
'm_time_column',
'm_time_points',
'm_id_column')
## inputs <- list()
for (dir_ui in m_dir_uis)
inputs[[dir_ui]] <- reactiveVal()
loading_ <- reactiveVal(FALSE)
loaded_ <- reactiveVal(FALSE)
#####
sc_metadata_label_ <- reactiveVal("")
sc_metadata_ <- reactiveVal()
choices_ <- reactiveVal()
observeEvent(input[['sc_metadata_file']],{
if (! loading_()) {
## showNotification(paste("input[['sc_metadata_file']]","inputs[['sc_metadata_file']](input[['sc_metadata_file']])"), duration = NULL)
inputs[['sc_metadata_file']](input[['sc_metadata_file']])
## print("set_file_ui('sc_metadata_file')")
## print(set_file_ui('sc_metadata_file'))
sc_metadata_label_(set_file_ui('sc_metadata_file'))
if (file.exists(sc_metadata_label_()) ) {
if (file_ext(sc_metadata_label_()) %in% c("rds", "RDS") ) {
cellInfo <- readRDS( sc_metadata_label_() )
if (!is.data.frame(cellInfo)){
showNotification("No metadata file",
type = "warning",
duration = 10)
cellInfo <- data.frame()
}
} else
cellInfo <- fread(sc_metadata_label_(), header=TRUE, data.table=FALSE)
} else {
showNotification("No metadata file",
type = "warning",
duration = 10)
# hideTab(inputId = "main_tabset",
# target = "Annotations")
# hideTab(inputId = "main_tabset",
# target = "Filters")
# hideTab(inputId = "main_tabset",
# target = "SC sampling depths")
# hideTab(inputId = "main_tabset",
# target = "Variants")
# hideTab(inputId = "main_tabset",
# target = "Inference")
# hideTab(inputId = "main_tabset",
# target = "Results")
cellInfo <- data.frame()
}
sc_metadata_(cellInfo)
if ( file.exists(sc_metadata_label_()) )
choices_(colnames(sc_metadata_()))
else
choices_(c(""))
id_col <- NULL
time_col <- NULL
if (length(choices_()) > 2) {
id_col <- choices_()[1]
time_col <- choices_()[2]
}
inputs[['m_id_column']](id_col)
inputs[['m_time_column']](time_col)
time_points <- NULL
if (!is.null(time_col))
time_points <- unique(as.character(sc_metadata_()[, time_col]))
inputs[['m_time_points']](time_points)
}
})
observeEvent(input[['m_id_column']], {
if (! loading_()) {
## showNotification(paste("input[['m_time_column']]","inputs[['m_time_column']](input[['m_time_column']])"), duration = NULL)
id_col <- input[['m_id_column']]
inputs[['m_id_column']](id_col)
if ((inputs[['m_time_column']]() == inputs[['m_id_column']]()) &&
!("" == inputs[['m_id_column']]()))
showNotification(paste("Same column for cell Id and time"),
type = "warning",
duration = 10)
## # id_points <- NULL
## # if ( id_col %in% colnames(sc_metadata_()) )
## # id_points <- unique(as.character(sc_metadata_()[, id_col]))
## # inputs[['m_id_points']](id_points)
}
})
observeEvent(input[['m_time_column']], {
if (! loading_()) {
time_col <- input[['m_time_column']]
inputs[['m_time_column']](time_col)
time_points <- NULL
if (time_col %in% colnames(sc_metadata_()) )
time_points <- unique(as.character(sc_metadata_()[, time_col]))
inputs[['m_time_points']](time_points)
if ((inputs[['m_time_column']]() == inputs[['m_id_column']]()) &&
!(""==inputs[['m_time_column']]()))
showNotification(paste("Same column for cell Id and time"),
type = "warning",
duration = 10)
}
})
observeEvent(input[['m_time_points']], {
if (! loading_()) {
inputs[['m_time_points']](input[['m_time_points']])
}
if (loading_() & loaded_()) {
loading_(FALSE)
loaded_(FALSE)
}
if (file.exists(sc_metadata_label_()) )
if (!is.null(input[['m_time_points']]))
if (length(input[['m_time_points']]) > 1) {
# showTab(inputId = "main_tabset",
# target = "Annotations")
# showTab(inputId = "main_tabset",
# target = "Filters")
# showTab(inputId = "main_tabset",
# target = "SC sampling depths")
# showTab(inputId = "main_tabset",
# target = "Variants")
# showTab(inputId = "main_tabset",
# target = "Inference")
}
})
observeEvent(input[["pr_next"]],{ # The previous does not trigger the event for consecutive load
if ( file.exists(sc_metadata_label_()) )
if (!is.null(input[['m_time_points']]))
if (length(input[['m_time_points']]) > 1) {
# showTab(inputId = "main_tabset",
# target = "Annotations")
# showTab(inputId = "main_tabset",
# target = "Filters")
# showTab(inputId = "main_tabset",
# target = "SC sampling depths")
# showTab(inputId = "main_tabset",
# target = "Variants")
# showTab(inputId = "main_tabset",
# target = "Inference")
}
# delay(1000,
# updateTabsetPanel(session, "main_tabset", selected = "SC metadata")
# )
})
observeEvent(inputs[['sc_metadata_file']](), {
## update the file select button name
## showNotification(paste("inputs[['sc_metadata_file']]","updateActionButton"), duration = NULL)
updateActionButton(session,
'sc_metadata_file',
label = set_file_ui('sc_metadata_file'))
})
### problema update ma necessario
observeEvent(inputs[['m_time_column']](), {
## update time_col ui
## showNotification(paste("inputs[['m_time_column']]","updateSelectInput"), duration = NULL)
updateSelectInput(session,
"m_time_column",
## label = "Time column",
choices = choices_(),
selected = inputs[['m_time_column']]()
)
})
observeEvent(inputs[['m_id_column']](),{
## Update time_col ui
## showNotification(paste("inputs[['m_time_column']]","updateSelectInput"), duration = NULL)
updateSelectInput(session,
"m_id_column",
## label = "Cell id column",
choices = choices_(),
selected = inputs[['m_id_column']]()
)
})
######
observe({
hide(id = "m_idCol_div")
if (file.exists(sc_metadata_label_()) ) {
shinyjs::show(id="m_idCol_div")
}
})
observe({
hide(id = "m_timePointsCol_div")
if (file.exists(sc_metadata_label_()) ) {
shinyjs::show(id="m_timePointsCol_div")
}
})
## Time_column ui
output$m_idCol <-
renderUI(selectInput("m_id_column", "Cell id column", c("")) %>%
make_shiny_help_popover ("Ids column",
text[["m_idCol"]],
server = TRUE
)
)
output$m_timePointsCol <-
renderUI(selectInput("m_time_column", "Time column", c("")) %>%
make_shiny_help_popover ("Sampling times column",
text[["m_timePointsCol"]],
server = TRUE
)
)
## Time_points ui
output$m_timePoints <-
renderUI({
rank_list_basic <-
rank_list(text = "Drag the time points in chronological order (before the smaller times)",
labels = inputs[['m_time_points']](),
input_id = "m_time_points",
options = sortable_options(disabled = !is.null(inputs[["demo"]]()))
)
x <- rank_list_basic %>%
make_title_help_popover (tags$b("Sampling points"),
"Sampling time points",
text[["m_timePoints"]],
server = TRUE
)
if (loading_()) {
loaded_(TRUE)
}
x
})
observe({
hide(id = "m_timePoints_div")
if (file.exists(sc_metadata_label_()) )
shinyjs::show(id = "m_timePoints_div")
})
## output[['sc_metadata_file']] <- renderText(parseFilePaths(roots = roots_dir, inputs[['sc_metadata_file']]()))
output[['m_id_column_tab']] <-
renderTable(head(sc_metadata_()[inputs[['m_id_column']]()]),
bordered = TRUE,
rownames = TRUE)
output[['sc_metadata_file']] <-
renderPrint(inputs[['sc_metadata_file']]())
output[['m_time_column']] <-
renderText(inputs[['m_time_column']]())
output[['m_id_column']] <-
renderText(inputs[['m_id_column']]())
output[['m_time_points']] <-
renderText(inputs[['m_time_points']]())
## #output[['m_id_column']] <- renderPrint(inputs[['m_id_column']]())
## #output$cellInfo <- renderTable({
## # if ('root'%in%names(input$sc_metadata_file)){
## # inFile <- parseFilePaths(roots = roots_dir[input$sc_metadata_file[['root']]], input$sc_metadata_file)
## # if ( nrow(inFile)) {
## # #cellInfo <- read.csv(as.character(inFile$datapath))
## # cellInfo <- readRDS(as.character(inFile$datapath))
## # }
## # }
## #})
outputOptions(output, "m_timePoints", suspendWhenHidden = FALSE)
outs <- outputOptions(output)
lapply(names(outs),
function(name) {
outputOptions(output,
name,
suspendWhenHidden = FALSE)
})
#rs_(callr::r_session$new(options = sopt, wait = T))
#rs_()$supervise(T)
# rp <- callr::r_bg(
# func = long_job,
# args = list("port"=port),
# supervise = TRUE
#)
observeEvent(input[["res_refresh"]], {
#browser()
returned_vals <- show_result(rs_())
rs_(returned_vals$rs)
inputs[["res_lastrefresh"]](returned_vals$message)
})
output[["res_lastrefresh"]] <- renderText(inputs[["res_lastrefresh"]]())
}
shinyApp(ui, server)
## return (shinyApp(ui, server))
## runApp(system.file("shiny", "tooltip_popover_modal", package = "bsplus"))
##}
### end of file -- app.R
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