inst/Kronos_pre_processing/app.R
In CL-CHEN-Lab/User_interface_for_Kronos_scRT: R-package and Shiny App interface for the analysis of single cell replication timing data
#options
options(stringsAsFactors = FALSE,
dplyr.summarise.inform=FALSE,
warn = 1,
scipen = 999)
#load operator
`%>%` = tidyr::`%>%`
#set ggplot theme
ggplot2::theme_set(new = ggplot2::theme_bw())
#Java function to close this app
jscode <- "shinyjs.closeWindow = function() { window.close(); }"
#find max number of cores
maxCores = parallel::detectCores()
# Define UI
ui <- shinydashboard::dashboardPage(
title = 'Kronos scRT',
skin = 'red',
shinydashboard::dashboardHeader(title = shiny::span(
shiny::img(src = 'KronosLogo.png', width = '100%')
)),
shinydashboard::dashboardSidebar(
shinydashboard::sidebarMenu(
id = 'Sidebar',
shinydashboard::menuItem(text = "FastqToBam",
tabName = "Home"),
shinydashboard::menuItem(text = "FastqToBam Metrics",
tabName = "Metrics"),
shinydashboard::menuItem(text = "Binning",
tabName = "Binning"),
shinydashboard::menuItem(text = "Copy Number Calling",
tabName = "CN"),
shinydashboard::menuItem(text = "10XGenomics data conversion",
tabName = "10X"),
shinydashboard::menuItem(text = "Exit",
tabName = "Exit")
)
),
shinydashboard::dashboardBody(
#use shinyjs
shinyjs::useShinyjs(),
#to close window
shinyjs::extendShinyjs(text = jscode, functions = c("closeWindow")),
#use CSS
shiny::tags$head(
shiny::tags$link(rel = "stylesheet",
type = "text/css",
href = "custom.css")
),
#setting spinner
shinybusy::add_busy_spinner(
spin = "fading-circle",
position = 'bottom-right',
color = 'red',
height = '200px',
width = '200px'
),
shinydashboard::tabItems(#####home
{
shinydashboard::tabItem(tabName = "Home",
shiny::fluidPage(
shiny::fluidRow(
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyDirButton(
id = 'Fastq',
label = 'Fastq files folder',
title = 'Fastq files folder',
style = 'width:100%;'
)
),
shiny::column(width = 9, shiny::htmlOutput('Fastq_out'))
),
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyFilesButton(
id = 'index',
label = shiny::div(
'Bowtie2 index',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = "Select one of the index files. If you don't have a compiled index, you can download one from http://bowtie-bio.sourceforge.net/bowtie2." , placement = 'right')
),
title = 'Bowtie2 index',
style = 'width:100%;',
multiple = F
)
),
shiny::column(width = 9, shiny::htmlOutput('index_out'))
),
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyFilesButton(
id = 'Adapters',
label = shiny::div(
'Adapters list',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'A text files with one adapter per line with no header. If not provided Kronos will look for standard illumina adapters' , placement = 'right')
),
title = 'Adapters list',
style = 'width:100%;',
multiple = F
)
),
shiny::column(width = 9, shiny::htmlOutput('Adapters_out'))
),
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyDirButton(
id = 'out',
label = 'Output files folder',
title = 'Output files folder',
style = 'width:100%;'
)
),
shiny::column(width = 9, shiny::htmlOutput('Output_out'))
),
shiny::fluidRow(
shiny::column(
width = 3,
shiny::radioButtons(
inputId = 'reads_type',
label = 'Sequencing',
choices = c('PE', 'SE', 'PE to treat as SE'),
inline = T,
selected = 'PE',
width = '100%'
)
),
shiny::column(
width = 3,
shiny::numericInput(
inputId = 'min_size',
label = 'Read min size after trimming',
value = 25,
min = 15,
step = 1,
width = '100%'
)
),
shiny::column(
width = 3,
shiny::radioButtons(
inputId = 'phred33',
label = 'Quality score',
choiceValues = c(T, F) ,
choiceNames = c('phred33', 'phred64'),
selected = T,
inline = T,
width = '100%'
)
)
),
shiny::uiOutput('patter_sample'),
shiny::fluidRow(shiny::column(
width = 3,
shiny::sliderInput(
inputId = 'cores',
label = 'Cores to use',
min = 1,
max = maxCores,
value = trunc(maxCores / 2),
step = 1
)
)),
shiny::fluidRow(shiny::column(
width = 3,
shinyjs::disabled(
shiny::actionButton(
inputId = 'run',
label = 'Run',
width = '100%'
)
)
)),
shiny::fluidRow(shiny::column(width = 12,
shiny::htmlOutput('final')))
)
))
},
######metrics
{
shinydashboard::tabItem(
tabName = "Metrics",
shiny::fluidRow(
shiny::column(
width = 4,
align = 'center',
shinyFiles::shinyFilesButton(
id = 'Load_metrics',
label = 'Load old Metrics',
title = 'Load old Metrics',
multiple = F,
style = 'width:75%;'
)
),
shiny::column(
width = 4,
align = 'center',
shinyjs::disabled(
shinyFiles::shinySaveButton(
id = 'Save_plots',
label = 'Save diagnostic plot',
title = 'Save diagnostic plot',
filetype = '.pdf',
style = 'width:75%;'
)
)
),
shiny::column(
width = 4,
align = 'center',
shinyjs::disabled(
shinyFiles::shinySaveButton(
id = 'Save_table',
label = 'Save table',
title = 'Save table',
filetype = '.tsv',
style = 'width:75%;'
)
)
)
),
shiny::fluidRow(shiny::column(
width = 12,
shiny::plotOutput(
'final_plot1',
# click = shiny::clickOpts(id = 'final_plot_click1'),
brush = shiny::brushOpts(id = 'final_plot_brush1',
resetOnNew = T),
dblclick = shiny::dblclickOpts(id = 'final_plot_dclick1', clip = T, delay = 200)
)
)),
shiny::fluidRow(shiny::column(
width = 12,
shinyjs::hidden(
shiny::radioButtons(
inputId = 'final_table_selector',
label = 'Parameter',
choices = '',
inline = F,
width = '100%'
)
)
)),
shiny::fluidRow(shiny::column(
width = 12,
shiny::tableOutput('final_table')
))
)
},
#####binning
{
shinydashboard::tabItem(
tabName = "Binning",
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyFilesButton(
id = 'RefGenome_binning',
label = shiny::div(
'Reference genome fasta file',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = "For most genomes, fasta file can be downloaded from UCSC Genome Browser. N.B. you need to download the file containing all chromosomes." , placement = 'right')
),
title = 'Reference genome fasta file',
multiple = F,
style = 'width:100%;'
)
),
shiny::column(width = 9,
shiny::htmlOutput('RefGenome_binning_out'))
),
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyFilesButton(
id = 'index_binning',
label = shiny::div(
'Bowtie2 index',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = "Select one of the index files. If you don't have a compiled index, you can download one from http://bowtie-bio.sourceforge.net/bowtie2." , placement = 'right')
),
title = 'Bowtie2 index',
style = 'width:100%;',
multiple = F
)
),
shiny::column(width = 9, shiny::htmlOutput('index_binning_out'))
),
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyDirButton(
id = 'out_binning',
label = 'Output files folder',
title = 'Output files folder',
style = 'width:100%;'
)
),
shiny::column(width = 9, shiny::htmlOutput('Output_binning_out'))
),
shiny::fluidRow(
shiny::column(
width = 3,
shiny::radioButtons(
inputId = 'Param_binning',
label = 'Parameters estimation',
choices = c('Auto', 'Manual'),
selected = 'Auto',
inline = T,
width = '100%'
)
)),
shiny::uiOutput('Paramui_binning_out1'),
shiny::uiOutput('Paramui_binning_out2'),
shiny::fluidRow(
shiny::column(
width = 3,
shiny::sliderInput(
inputId = 'Coverage_binning',
label = shiny::div(
'Coverage',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'Simulated dept of sequencing to calculate bin mappability.' , placement = 'right')
),
min = 1,
max = 10,
value = 1,
step = 1,
post = 'X',
width = '100%'
)
),
shiny::column(
width = 3,
shiny::sliderInput(
inputId = 'BinSize_binning',
label = shiny::div(
'BinSize',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'Bin size that will be used to call CNV. This size does not correspond to the final scRT resolution. The bin size should increased if the average cell coverage is very low.' , placement = 'right')
),
min = 5,
max = 100,
value = 20,
step = 1,
post = 'kb',
width = '100%'
)
),
shiny::column(
width = 3,
shiny::sliderInput(
inputId = 'Cores_binning',
label = 'Cores',
min = 1,
max = maxCores,
value = trunc(maxCores / 2),
step = 1,
width = '100%'
)
)
),
shinydashboard::box(
title = 'Advanced options',
status = 'primary',
solidHeader = T,
width = '100%',
collapsible = T,
collapsed = T,
shiny::fluidRow(
shiny::column(
width = 3,
shiny::sliderInput(
inputId = 'Mappability_binning',
label = shiny::div(
'Acceptable mappability range',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'Bins with mappability higher or lower than the acceptable mappability range will be excluded from the analysis.' , placement = 'right')
),
min = 0.5,
max = 3,
value = c(0.8, 1.5),
step = 0.1,
width = '100%'
)
),
shiny::column(
width = 3,
shiny::sliderInput(
inputId = 'ErrorRate_binning',
label = shiny::div(
'Sequencer Error Rate',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'Is the error rate of the sequencer you used to sequence your data. This parameter is used to simulates reads and calculate the bin mappability.' , placement = 'right')
),
min = 0,
max = 0.3,
value = 0.1,
post = '%',
step = 0.001,
width = '100%'
)
)
),
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyFilesButton(
id = 'Blacklist_binning',
label = shiny::div(
'Blacklist',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'Because of their repetitive nature, some regions of the genome are difficult to map. The user can hide these regions form the analysis providing a blacklist file. Such lists are available in literature. Some useful ones can be found at https://github.com/Boyle-Lab/Blacklist' , placement = 'right')
),
title = 'Blacklist',
multiple = F
)
),
shiny::column(width = 9,
shiny::htmlOutput('Blacklist_binning_out'))
)
),
shiny::fluidRow(
shiny::column(
width = 3,
shiny::textInput(
inputId = 'chr_prefix_binning',
label = shiny::div(
'Chromosome prefix',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'Depending on your reference genome, chromosomes or scaffolds could be named differently. Please, provide the prefix that precedes the chromosome or scaffold number. If no prefix is present this box has to be emptied.' , placement = 'right')),
value = 'chr',
width = '100%'
)
),
shiny::column(
width = 3,
shiny::textInput(
inputId = 'chr_range_binning',
label = shiny::div(
'Chromosomes to consider',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'Chromosome to include in the analysis. You can define ranges using ":" and individual chromosomes using ",". Don\'t include the chr prefix!' , placement = 'right')
),
value = '1:22',
width = '100%'
)
)
),
shiny::fluidRow(shiny::column(
width = 3,
shinyjs::disabled(
shiny::actionButton(
inputId = 'run_binning',
label = 'Run',
width = '100%'
)
)
))
)
},
#####CN
{
shinydashboard::tabItem(
tabName = "CN",
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyFilesButton(
id = 'Bins_CN',
label = div('Bins file',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'Bins file created during the binning step.' , placement = 'right')),
title = 'Bins file',
style = 'width:100%;',
multiple = F
)
),
shiny::column(width = 9,
shiny::htmlOutput('Bins_CN'))
),
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyFilesButton(
id = 'ChrSize_CN',
label = shiny::div(
'Chrom size file',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'For most genome assemblies this file can be downloaded from UCSC Genome Browser website.' , placement = 'right')),
title = 'Chrom size file',
style = 'width:100%;',
multiple = F
)
),
shiny::column(width = 9,
shiny::htmlOutput('ChrSize_CN'))
),
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyDirButton(
id = 'Output_CN',
label = 'Results folder',
title = 'Results folder',
style = 'width:100%;'
)
),
shiny::column(width = 9,
shiny::htmlOutput('Output_CN'))
),
shiny::fluidRow(
shiny::column(
width = 3,
shiny::textInput(
inputId = 'CHR_CN',
label = shiny::div('Chromosome prefix',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'Depending on your reference genome, chromosomes or scaffolds could be named differently. Please, provide the prefix that precedes the chromosome or scaffold number. If no prefix is present this box has to be emptied.' , placement = 'right')
),
value = 'chr',
width = '100%'
)
),
shiny::column(
width = 3,
shiny::textInput(
inputId = 'CHR_RANGE_CN',
label = shiny::div(
'Chromosomes to consider',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'Chromosome to include in the analysis. You can define ranges using ":" and individual chromosomes using ",". Don\'t include the chr prefix!' , placement = 'right')
),
value = '1:22',
width = '100%'
)
),
shiny::column(
width = 3,
shiny::sliderInput(
inputId = 'Cores_CN',
label = 'Number of cores',
min = 1,
max = maxCores,
value = trunc(maxCores / 2),
step = 1
)
)
),
shinydashboard::box(
title = 'Advanced options',
status = 'primary',
solidHeader = T,
width = 12,
collapsible = T,
collapsed = T,
shiny::fluidRow(shiny::column(
width = 3,
shiny::numericInput(
inputId = 'min_reads_CN',
label = shiny::div('Min number of reads per cell',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'This threshold depends on the genome size of your cells and on the chromosomes you want to keep in the analysis.' , placement = 'right')
),
value = 2 * 10 ^ 5,
step = 10 ^ 4,
width = '100%'
)
)),
shiny::fluidRow(shiny::column(
width = 12,
shiny::radioButtons(
inputId = 'Ploidy_Restrictions_CN',
label = div('Ploidy restrictions',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'If Fix Ploidy Range is selected, the software selects the most appropriated ploidy in the range and calculates the associated confidence. If Fix Average Ploidy is selected, cells are imposed the closest possible ploidy to the average one and does not calculate the confidence of this calling.' , placement = 'right')
),
choices = c('Fix Average Ploidy', 'Fix Ploidy Range'),
inline = T,
selected = 'Fix Ploidy Range',
width = '100%'
)
)),
shiny::uiOutput('FixAveragePloidy'),
shiny::uiOutput('FixPloidyRange')
),
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyDirButton(
id = 'Bamdir_CN',
label = 'Bam files folder',
title = 'Bam files folder',
style = 'width:100%;'
)
),
column(width = 9,
shiny::htmlOutput('Bamdir_CN'))
),
shiny::fluidRow(
shiny::column(
width = 3,
shiny::textInput(
inputId = 'basename_CN',
label = shiny::div('Sample basename',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'This Name identifies each individual experiment. It can be modified later on in the analysis.' , placement = 'right')),
value = 'Exp',
width = '100%'
)
),
shiny::column(
width = 3,
shiny::textInput(
inputId = 'group_CN',
label = shiny::div('Sample group',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'If cells have been sequenced in different experiments, providing the same group name allows to merge them after normalization. It can be modified later on in the analysis.' , placement = 'right')),
value = 'Exp',
width = '100%'
)
)
),
shiny::fluidRow(shiny::column(
width = 3,
shinyjs::disabled(
shiny::actionButton(
inputId = 'AddSample_CN',
label = 'Add Sample',
width = '100%'
)
)
)),
shiny::fluidRow(shiny::column(
width = 9,
shiny::tableOutput('Samples_CN')
)),
shiny::fluidRow(shiny::column(
width = 3,
shinyjs::disabled(
shiny::actionButton(
inputId = 'Run_CN',
label = 'Run',
width = '100%'
)
)
))
)
},
#####10X
{
shinydashboard::tabItem(
tabName = "10X",
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyFilesButton(
id = 'PerCell_10X',
label = div('PerCell',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = '10XGenomics per_cell_summary_metrics.csv' , placement = 'right')),
title = 'PerCell file',
style = 'width:100%;',
multiple = F
)
),
shiny::column(width = 9,
shiny::htmlOutput('PerCell_10X'))
),
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyFilesButton(
id = 'CNV_10X',
label = shiny::div(
'CNV',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = '10XGenomics node_cnv_calls.bed' , placement = 'right')),
title = 'CNV_10X',
style = 'width:100%;',
multiple = F
)
),
shiny::column(width = 9,
shiny::htmlOutput('CNV_10X'))
),
shiny::fluidRow(
shiny::column(
width = 3,
shiny::textInput(
inputId = 'Basename_10X',
label = 'Basename',
value = 'Exp',
width = '100%'
)
),
shiny::column(
width = 3,
shiny::textInput(
inputId = 'Group_10X',
label = 'Group',
value = 'Exp',
width = '100%'
)
)),
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyDirButton(
id = 'Output_10X',
label = 'Results folder',
title = 'Results folder',
style = 'width:100%;'
)
),
shiny::column(width = 9,
shiny::htmlOutput('Output_10X'))
),
shiny::fluidRow(
shiny::column(
width = 3,
shinyjs::disabled(
shiny::actionButton(inputId = 'Run_10X',label = 'Run',width = '100%'))
)
)
)
})
)
)
server <- function(input, output, session) {
#define operators
`%>%` = tidyr::`%>%`
`%do%` = foreach::`%do%`
`%dopar%` = foreach::`%dopar%`
#find max number of cores
maxCores = parallel::detectCores()
#set roots
roots = c(shinyFiles::getVolumes()(),
Home = Sys.getenv("HOME"))
#set shinyFiles buttons
shinyFiles::shinyDirChoose(
input = input,
id = 'Fastq',
session = session,
roots = roots,
defaultRoot = 'Home'
)
shinyFiles::shinyDirChoose(
input = input,
id = 'out',
session = session,
roots = roots,
defaultRoot = 'Home'
)
shinyFiles::shinyFileChoose(
input = input,
id = 'index',
session = session,
roots = roots,
defaultRoot = 'Home'
)
shinyFiles::shinyFileChoose(
input = input,
id = 'Adapters',
session = session,
roots = roots,
defaultRoot = 'Home'
)
shinyFiles::shinyFileChoose(
input = input,
id = 'fasta',
session = session,
roots = roots,
defaultRoot = 'Home'
)
shinyFiles::shinyDirChoose(
input = input,
id = 'Output_10X',
session = session,
roots = roots,
defaultRoot = 'Home'
)
shinyFiles::shinyFileChoose(
input = input,
id = 'CNV_10X',
session = session,
roots = roots,
defaultRoot = 'Home'
)
shinyFiles::shinyFileChoose(
input = input,
id = 'PerCell_10X',
session = session,
roots = roots,
defaultRoot = 'Home'
)
#define variables
variables = reactiveValues(
File1 = NULL,
File2 = NULL,
Adapters = NULL,
out = NULL,
fastq_dir = NULL,
index = NULL,
activate_start1 = F,
activate_start2 = F,
activate_start3 = F,
proceed_run = F,
info = dplyr::tibble()
)
variables_binning = reactiveValues(
fasta = NULL,
index = NULL,
out = NULL,
Bam_dir = NULL,
blacklist = NULL,
activate_start1 = F,
activate_start2 = F,
activate_start3 = F,
activate_start4 = F,
activate_start5 = T,
read_size = 40,
frag_size = 200,
read_type = 'PE'
)
variables_10X = reactiveValues(
Output_10X=NULL,
PerCell_10X=NULL,
CNV_10X=NULL,
)
###10X to Kronos
{
#set output folder
shiny::observeEvent(input$Output_10X, {
if (!is.numeric(input$Output_10X)) {
variables_10X$Output_10X = shinyFiles::parseDirPath(roots = roots, selection = input$Output_10X)
} else{
variables_10X$Output_10X = NULL
}
output$Output_10X = shiny::renderText(variables_10X$Output_10X)
})
#set PerCell_10X
shiny::observeEvent(input$PerCell_10X, {
if (!is.numeric(input$PerCell_10X)) {
variables_10X$PerCell_10X = shinyFiles::parseFilePaths(roots = roots, selection = input$PerCell_10X)
variables_10X$PerCell_10X = variables_10X$PerCell_10X$datapath
variables_10X$PerCell_10X = Kronos.scRT::right_format(
file_path = variables_10X$PerCell_10X,
delim = ',',
columns_to_check = c(
"barcode",
"cell_id",
"total_num_reads",
"num_unmapped_reads" ,
"num_lowmapq_reads",
"num_duplicate_reads" ,
"num_mapped_dedup_reads",
"frac_mapped_duplicates",
"effective_depth_of_coverage",
"effective_reads_per_1Mbp" ,
"raw_mapd",
"normalized_mapd" ,
"raw_dimapd",
"normalized_dimapd" ,
"mean_ploidy",
"ploidy_confidence" ,
"is_high_dimapd",
"is_noisy"
),
wrong_message = paste(
'<b><p style="color:#FF0000";>',
variables_10X$PerCell_10X,
'does not have the right format!</p></b>'
),
rigth_message = variables_10X$PerCell_10X
)
} else{
variables_10X$PerCell_10X = NULL
}
output$PerCell_10X = shiny::renderText(variables_10X$PerCell_10X)
})
#set CN_10X
shiny::observeEvent(input$CNV_10X, {
if (!is.numeric(input$CNV_10X)) {
variables_10X$CNV_10X = shinyFiles::parseFilePaths(roots = roots, selection = input$CNV_10X)
variables_10X$CNV_10X = variables_10X$CNV_10X$datapath
variables_10X$CNV_10X = Kronos.scRT::right_format(
file_path = variables_10X$CNV_10X,
delim = '\t',skip = 2,
columns_to_check = c(
"#chrom",
"start",
"end",
"id",
"copy_number",
"event_confidence"
),
wrong_message = paste(
'<b><p style="color:#FF0000";>',
variables_10X$CNV_10X,
'does not have the right format!</p></b>'
),
rigth_message = variables_10X$CNV_10X
)
} else{
variables_10X$CNV_10X = NULL
}
output$CNV_10X = shiny::renderText(variables_10X$CNV_10X)
})
#basename and group
shiny::observeEvent(input$Group_10X, {
shiny::updateTextInput(inputId = 'Group_10X',value = stringr::str_replace(string = input$Group_10X,pattern = ' ',replacement = '_'))
})
shiny::observeEvent(input$Basename_10X, {
shiny::updateTextInput(inputId = 'Basename_10X',value = stringr::str_replace(string = input$Basename_10X,pattern = ' ',replacement = '_'))
})
#allow to run if files are selected
shiny::observeEvent(c(
variables_10X$Output_10X,
variables_10X$PerCell_10X,
variables_10X$CNV_10X
),
{
if(!is.null(variables_10X$Output_10X) &
!is.null(variables_10X$PerCell_10X)&
!is.null(variables_10X$CNV_10X)){
shinyjs::enable('Run_10X')
}else{
shinyjs::disable('Run_10X')
}
})
#run conversion
shiny::observeEvent(input$Run_10X,{
results=Kronos.scRT::TenXtoKronos(PerCell = variables_10X$PerCell_10X,CNV =variables_10X$CNV_10X,basename = input$Basename_10X, input$Group_10X)
results$PerCell%>%
readr::write_csv(paste0(file.path(variables_10X$Output_10X, 'Kronos_format_'), basename(variables_10X$PerCell_10X)))
results$CNV%>%
readr::write_tsv(paste0(file.path(variables_10X$Output_10X, 'Kronos_format_'), stringr::str_replace(string = basename(variables_10X$CNV_10X),pattern = '.bed',replacement = '.tsv')))
shiny::updateTextInput(inputId = 'Group_10X',value = 'Exp')
shiny::updateTextInput(inputId = 'Basename_10X',value = 'Exp')
variables_10X$PerCell_10X=NULL
variables_10X$CNV_10X=NULL
output$CNV_10X = shiny::renderText(variables_10X$CNV_10X)
output$PerCell_10X = shiny::renderText(variables_10X$PerCell_10X)
})
}
##fastqToBam
{
#stop app when the session ends
session$onSessionEnded(function() {
shiny::stopApp()
})
#load tex input if PE format
shiny::observeEvent(input$reads_type, {
if (input$reads_type != 'SE') {
output$patter_sample = shiny::renderUI({
shiny::fluidRow(column(
width = 3,
shiny::textInput(
inputId = 'R1',
label = 'Pattern to identify R1 fastq',
value = '_R1'
)
),
column(
width = 3,
shiny::textInput(
inputId = 'R2',
label = 'Pattern to identify R2 fastq',
value = '_R2'
)
))
})
} else{
output$patter_sample = shiny::renderUI({
NULL
})
}
})
###select fastq folder
shiny::observeEvent(input$Fastq, {
output$final <- shiny::renderText(NULL)
if (!is.numeric(input$Fastq)) {
#recover fastq directory
variables$fastq_dir = shinyFiles::parseDirPath(selection = input$Fastq, roots = roots)
#check for fastq files
if (length(list.files(path = variables$fastq_dir, pattern = 'fastq|fq')) >
0) {
output$Fastq_out <- shiny::renderText(variables$fastq_dir)
variables$activate_start1 = T
} else{
output$Fastq_out <-
shiny::renderText(
paste(
'<b><p style="color:#FF0000";> selected directory does not contain fastq files</b></p>'
)
)
variables$activate_start1 = F
}
} else{
variables$activate_start1 = F
output$Fastq_out <- shiny::renderText(NULL)
}
})
###select index
shiny::observeEvent(input$index, {
output$final <- shiny::renderText(NULL)
if (!is.numeric(input$index)) {
#recover index directory
variables$index = shinyFiles::parseFilePaths(selection = input$index, roots = roots)
variables$index = variables$index$datapath
#check that the selected file is actually part of an index
if (stringr::str_detect(string = variables$index, pattern = '.bt2')) {
variables$index = stringr::str_remove(variables$index, pattern = '.[0-9]{1,2}.bt2|.rev.[0-9]{1,2}.bt2')
output$index_out <- shiny::renderText(variables$index)
variables$activate_start3 = T
} else{
output$index_out <-
shiny::renderText(
paste(
'<b><p style="color:#FF0000";> selected file does not belong to a bowtie2 index.</b></p>'
)
)
variables$activate_start3 = F
}
} else{
variables$activate_start3 = F
output$index_out <-
shiny::renderText(NULL)
}
})
###select adapter
shiny::observeEvent(input$Adapters,
{
if (!is.numeric(input$Adapters))
{
#recover index directory
variables$Adapters = shinyFiles::parseFilePaths(selection = input$Adapters, roots = roots)
variables$Adapters = variables$Adapters$datapath
#check that the selected file is actually part of an index
if (Kronos.scRT::right_format(
file_path = variables$Adapters,
columns_to_check = 1,
logical = T
)) {
variables$Adapters = readr::read_lines(variables$Adapters)
output$Adapters_out <-
shiny::renderText(variables$Adapters)
} else
{
output$Adapters_out <-
shiny::renderText(
paste(
'<b><p style="color:#FF0000";> Adapters file has to be a text file with one adapter per line, No header!</b></p>'
)
)
}
}
})
###select out folder
shiny::observeEvent(input$out,
{
output$final <- shiny::renderText(NULL)
if (!is.numeric(input$out))
{
#recover fastq directory
variables$out = shinyFiles::parseDirPath(selection = input$out, roots = roots)
#check for fastq files
if (length(list.files(path = variables$out)) == 0)
{
output$Output_out <- shiny::renderText(variables$out)
variables$activate_start2 = T
} else{
output$Output_out <-
shiny::renderText(
paste(
'<b><p style="color:#FF0000";> selected directory is not empty</b></p>'
)
)
variables$activate_start2 = F
}
} else{
variables$activate_start2 = F
output$Output_out <-
shiny::renderText(NULL)
}
})
##activate start
shiny::observeEvent(
c(
variables$activate_start1,
variables$activate_start2,
variables$activate_start3
),
{
if (variables$activate_start1 &
variables$activate_start2 &
variables$activate_start3)
{
shinyjs::enable('run')
} else
{
shinyjs::disable('run')
}
}
)
###start
shiny::observeEvent(input$run,
{
if (input$run > 0)
{
#disable all buttons till the end of the run
shinyjs::disable('run')
shinyjs::disable('Fastq')
shinyjs::disable('out')
shinyjs::disable('reads_type')
shinyjs::disable('cores')
shinyjs::disable('Adapters')
shinyjs::disable('index')
all_files = list.files(
path = variables$fastq_dir,
pattern = 'fastq|fq',
ignore.case = T,
full.names = T
)
if (input$reads_type == 'PE')
{
R1 = stringr::str_detect(string = basename(all_files),
pattern = input$R1)
R2 = stringr::str_detect(string = basename(all_files),
pattern = input$R2)
variables$File1 = all_files[R1]
variables$File2 = all_files[R2]
#check if file names order is matching
if (all(
stringr::str_split(
string = variables$File1,
pattern = input$R1,
simplify = T
)
[, 1] == stringr::str_split(
string = variables$File2,
pattern = input$R2,
simplify = T
)[, 1]
)) {
variables$proceed_run = T
} else
{
variables$proceed_run = F
}
} else
if (input$reads_type == 'SE')
{
variables$File1 = all_files
variables$proceed_run = T
} else
{
R1 = stringr::str_detect(string = all_files, pattern = input$R1)
R2 = stringr::str_detect(string = all_files, pattern = input$R2)
variables$File1 = all_files[R1]
variables$File2 = all_files[R2]
#check if file names order is matching
if (all(
stringr::str_split(
string = variables$File1,
pattern = input$R1,
simplify = T
)
[, 1] == stringr::str_split(
string = variables$File2,
pattern = input$R2,
simplify = T
)[, 1]
)) {
variables$proceed_run = T
cl = snow::makeCluster(input$cores)
doSNOW::registerDoSNOW(cl)
shiny::isolate({
file1 = variables$File1
file2 = variables$File2
out = variables$out
})
variables$File1 = foreach::foreach(i = 1:length(variables$File1)) %dopar%
{
Kronos.scRT::mergefastq(
FileList = c(file1[i], file2[i]),
output = file.path(out, 'MergedFastq')
)
}
snow::stopCluster(cl)
variables$File2 = NULL
variables$File1 = unlist(variables$File1)
variables$proceed_run = T
} else{
variables$proceed_run = F
}
}
if (variables$proceed_run) {
if (input$reads_type == 'PE') {
variables$info = Kronos.scRT::FastqToBam(
bowtie2_index = variables$index,
File1 = variables$File1,
File2 = variables$File2,
outputdir = variables$out,
adapters_list = variables$Adapters,
cores = input$cores,
Read_min_size_after_trimming = input$min_size,
phred33 = input$phred33
)
} else{
variables$info = Kronos.scRT::FastqToBam(
bowtie2_index = variables$index,
File1 = variables$File1,
outputdir = variables$out,
adapters_list = variables$Adapters,
cores = input$cores,
Read_min_size_after_trimming = input$min_size,
phred33 = input$phred33
)
}
#save info
variables$info %>% readr::write_tsv(file = file.path(variables$out, 'FastqToBamMetrics.tsv'))
shinydashboard::updateTabItems(session = session,
inputId = 'Sidebar',
selected = 'Metrics')
} else {
output$final_plot1 <-
shiny::renderPlot({
NULL
})
output$final_table <-
shiny::renderTable({
NULL
})
output$final <-
shiny::renderText(
'<b><p style="color:#FF0000";> files do not match, check your fastq folder.</b></p>'
)
}
#enable all buttons but run at the end of the run
shinyjs::enable('Fastq')
shinyjs::enable('out')
shinyjs::enable('reads_type')
shinyjs::enable('cores')
shinyjs::enable('Adapters')
shinyjs::enable('index')
}
})
####exit
{
shiny::observeEvent(input$Sidebar,
{
if (input$Sidebar == 'Exit') {
shinyjs::js$closeWindow()
shiny::stopApp()
}
})
}
}
####metrics
{
#shinyFiles buttons
shinyFiles::shinyFileSave(
input = input,
id = 'Save_plots',
session = session,
defaultRoot = 'Home',
roots = roots
)
shinyFiles::shinyFileSave(
input = input,
id = 'Save_table',
session = session,
defaultRoot = 'Home',
roots = roots
)
shinyFiles::shinyFileChoose(
input = input,
id = 'Load_metrics',
session = session,
defaultRoot = 'Home',
roots = roots
)
#upload data
shiny::observeEvent(input$Load_metrics, {
if (!is.numeric(input$Load_metrics)) {
#recover path and upload data
path = shinyFiles::parseFilePaths(roots = roots, selection = input$Load_metrics)
#check type
if (Kronos.scRT::right_format(
file_path = path$datapath,
columns_to_check = c('File', 'Parameter', 'Values', 'Category'),
logical = T
)) {
variables$Metrics = readr::read_tsv(path$datapath) %>%
dplyr::mutate(
Parameter = factor(Parameter, levels = unique(Parameter)),
Category = factor(Category, levels = unique(Category)),
x = ifelse(
Category %in% c('Total Reads', 'Unmapped Fraction', 'Proper Pair'),
1,
as.numeric(Category)
) + sample(
seq(-0.2, 0.2, 0.001),
size = dplyr::n(),
replace = T
)
) %>%
dplyr::ungroup()
#initialize Plot_selection
variables$Metrics$Color = 'red'
#active buttons
shinyjs::enable('Save_plots')
shinyjs::enable('Save_table')
#update select parameters
shiny::updateRadioButtons(
session = session,
inputId = 'final_table_selector',
choices = unique(variables$Metrics$Parameter),
inline = T
)
shinyjs::show('final_table_selector')
} else{
output$final_plot1 <- shiny::renderPlot(NULL)
output$final_table <- shiny::renderText('Wrong File!')
shinyjs::disable('Save_plots')
shinyjs::disable('Save_table')
shinyjs::hide('final_table_selector')
}
}
})
shiny::observeEvent(variables$info, {
if (nrow(variables$info) > 0) {
#add x variability for plotting
variables$Metrics = variables$info %>%
dplyr::mutate(
Category = factor(Category, levels = unique(Category)),
x = ifelse(
Category %in% c('Total Reads', 'Unmapped Fraction', 'Proper Pair'),
1,
as.numeric(Category)
) + sample(
seq(-0.2, 0.2, 0.001),
size = dplyr::n(),
replace = T
)
) %>%
dplyr::ungroup()
#initialise Plot_selection
variables$Metrics$Color = 'red'
#active buttons
shinyjs::enable('Save_plots')
shinyjs::enable('Save_table')
shiny::updateRadioButtons(
session = session,
inputId = 'final_table_selector',
choices = unique(variables$info$Parameter),
inline = T
)
shinyjs::show('final_table_selector')
}
})
#brush plot 1
shiny::observeEvent(input$final_plot_brush1, {
if (!is.null(input$final_plot_brush1)) {
#selected files
Files = variables$Metrics %>%
dplyr::filter(
Parameter == input$final_plot_brush1$panelvar1,
Values >= input$final_plot_brush1$ymin,
Values <= input$final_plot_brush1$ymax,
x >= input$final_plot_brush1$xmin,
x <= input$final_plot_brush1$xmax
) %>% dplyr::pull(File)
variables$Metrics = variables$Metrics %>%
dplyr::mutate(Color = ifelse(File %in% Files, 'red', 'black'))
}
})
#reset with dbclick
shiny::observeEvent(input$final_plot_dclick1,
{
#initialize reset
variables$Metrics = variables$Metrics %>%
dplyr::mutate(Color = 'red')
})
#if something has been selected
shiny::observeEvent(variables$Metrics, {
variables$plot1 = variables$Metrics %>%
dplyr::arrange(Color) %>%
ggplot2::ggplot() +
ggplot2::geom_boxplot(
ggplot2::aes(Category, Values),
outlier.size = 0,
outlier.colour = NA,
width = 0.8
) +
ggplot2::geom_point(ggplot2::aes(x, Values, color = Color), alpha =
0.5) +
ggplot2::theme_bw() +
ggplot2::labs(x = '', y = '') +
ggplot2::theme(
legend.position = 'none',
axis.text.x = ggplot2::element_text(
angle = 45,
hjust = 1,
vjust = 1
)
) +
ggplot2::scale_y_continuous(
labels = function(x)
sprintf(fmt = '%.1f', x)
) +
ggforce::facet_row(
~ Parameter,
scales = 'free',
space = 'free',
strip.position = 'right'
) +
ggplot2::scale_color_manual(values = c('red' = 'red', 'black', 'black'))
output$final_plot1 <-
shiny::renderPlot({
variables$plot1
})
})
shiny::observeEvent(c(variables$Metrics, input$final_table_selector), {
if (input$final_table_selector != '') {
output$final_table <-
shiny::renderTable(
variables$Metrics %>%
dplyr::filter(Parameter == input$final_table_selector,
Color == 'red') %>%
dplyr::select(-x, -Color) %>%
tidyr::spread(Category, Values)
)
}
})
##save
shiny::observeEvent(input$Save_plots, {
if (!is.numeric(input$Save_plots)) {
path = shinyFiles::parseSavePath(roots = roots, selection = input$Save_plots)
ggplot2::ggsave(
filename = path$datapath,
plot = variables$plot1,
device = grDevices::cairo_pdf,
width = 12,
height = 5
)
}
})
shiny::observeEvent(input$Save_table, {
if (!is.numeric(input$Save_table)) {
path = shinyFiles::parseSavePath(roots = roots, selection = input$Save_table)
variables$Metrics %>%
dplyr::select(-x, -Color) %>%
readr::write_tsv(file = path$datapath)
}
})
}
### Binning
{
#ui for auto selection of parameters
output$Paramui_binning_out1 = shiny::renderUI({
shiny::req(input$Param_binning == 'Auto')
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyDirButton(
id = 'Bam_binning',
label = 'Bam Files directory',
title = 'Bam Files directory',
style = 'width:100%;'
)
),
shiny::column(width = 6,
shiny::htmlOutput('Bam_binning_out'))
)
})
#ui for auto selection of parameters
output$Paramui_binning_out2 = shiny::renderUI({
shiny::req(input$Param_binning == 'Manual')
shiny::fluidRow(
shiny::column(
width = 3,
shiny::radioButtons(
inputId = 'Reads_type_binning',
label = 'Reads type',
choices = c('PE', 'SE'),
selected = variables_binning$read_type,
inline = T,
width = '100%'
)
),
shiny::column(
width = 3,
shiny::sliderInput(
inputId = 'Read_size_binning',
label = 'Read size',
min = 20,
max = 300,
value = variables_binning$read_size,
step = 1,
width = '100%'
)
),
shiny::column(width = 3,
shiny::uiOutput('Reads_type_binning'))
)
})
output$Reads_type_binning = shiny::renderUI({
shiny::req(input$Reads_type_binning == 'PE')
shiny::sliderInput(
inputId = 'Fragment_size_binning',
label = 'Fragment size',
min = 0,
max = 1000,
value = variables_binning$frag_size,
step = 1,
width = '100%'
)
})
#set shinyfiles
shinyFiles::shinyDirChoose(
input = input,
id = 'Bam_binning',
session = session,
roots = roots,
defaultRoot = 'Home'
)
shinyFiles::shinyFileChoose(
input = input,
id = 'RefGenome_binning',
session = session,
roots = roots,
defaultRoot = 'Home'
)
shinyFiles::shinyFileChoose(
input = input,
id = 'index_binning',
session = session,
roots = roots,
defaultRoot = 'Home'
)
shinyFiles::shinyDirChoose(
input = input,
id = 'out_binning',
session = session,
roots = roots,
defaultRoot = 'Home'
)
shinyFiles::shinyFileChoose(
input = input,
id = 'Blacklist_binning',
session = session,
roots = roots,
defaultRoot = 'Home'
)
# if manual setting is put on SE hide fragment size
shiny::observeEvent(input$Reads_type_binning, {
if (input$Reads_type_binning == 'SE') {
shinyjs::hide('Fragment_size_binning')
} else{
shinyjs::show('Fragment_size_binning')
}
})
#select fasta file
shiny::observeEvent(input$RefGenome_binning, {
if (!is.numeric(input$RefGenome_binning)) {
#recover path
variables_binning$fasta = shinyFiles::parseFilePaths(roots = roots,
selection = input$RefGenome_binning)
variables_binning$fasta = variables_binning$fasta$datapath
output$RefGenome_binning_out = shiny::renderText({
variables_binning$fasta
})
# first step to activate run
variables_binning$activate_start1 = T
} else{
variables_binning$fasta = NULL
output$RefGenome_binning_out = shiny::renderText({
variables_binning$fasta
})
variables_binning$activate_start1 = F
}
})
###select index
shiny::observeEvent(input$index_binning, {
if (!is.numeric(input$index_binning)) {
#recover index directory
variables_binning$index = shinyFiles::parseFilePaths(selection = input$index_binning,
roots = roots)
variables_binning$index = variables_binning$index$datapath
#check that the selected file is actually part of an index
if (stringr::str_detect(string = variables_binning$index, pattern = '.bt2')) {
variables_binning$index = stringr::str_remove(variables_binning$index, pattern = '.[0-9]{1,2}.bt2|.rev.[0-9]{1,2}.bt2')
output$index_binning_out <-
shiny::renderText(variables_binning$index)
variables_binning$activate_start2 = T
} else{
output$index_binning_out <-
shiny::renderText(
paste(
'<b><p style="color:#FF0000";> selected file does not belong to a bowtie2 index.</b></p>'
)
)
variables$activate_start2 = F
}
} else{
variables$activate_start2 = F
output$index_binning_out <-
shiny::renderText(NULL)
}
})
###select out folder
shiny::observeEvent(input$out_binning,
{
if (!is.numeric(input$out_binning)) {
#recover out directory
variables_binning$out = shinyFiles::parseDirPath(selection = input$out_binning, roots = roots)
#render out dir
output$Output_binning_out <-
shiny::renderText(variables_binning$out)
variables_binning$activate_start3 = T
} else{
variables_binning$activate_start3 = F
output$Output_binning_out <-
shiny::renderText(NULL)
}
})
#select bamfile folder
shiny::observeEvent(input$Bam_binning, {
if (!is.numeric(input$Bam_binning)) {
#recover fastq directory
variables_binning$Bam_dir = shinyFiles::parseDirPath(selection = input$Bam_binning, roots = roots)
#check for fastq files
if (length(list.files(path = variables_binning$Bam_dir, pattern = '.bam')) >
0) {
output$Bam_binning_out <-
shiny::renderText(variables_binning$Bam_dir)
variables_binning$activate_start4 = T
} else{
output$Bam_binning_out <-
shiny::renderText(
paste(
'<b><p style="color:#FF0000";> selected directory does not contain fastq files</b></p>'
)
)
variables_binning$activate_start4 = F
}
} else{
variables_binning$activate_start4 = F
output$Bam_binning_out <-
shiny::renderText(NULL)
variables_binning$Bam_dir = NULL
}
})
#activate start4 if Manual parameters are selected
shiny::observeEvent(input$Param_binning, {
if (input$Param_binning == 'Auto') {
variables_binning$activate_start4 = F
} else{
variables_binning$activate_start4 = T
}
})
#select blacklist
shiny::observeEvent(input$Blacklist_binning, {
if (!is.numeric(input$Blacklist_binning)) {
#recover index directory
variables_binning$blacklist = shinyFiles::parseFilePaths(selection = input$Blacklist_binning,
roots = roots)
variables_binning$blacklist = variables_binning$blacklist$datapath
#check that the selected file is actually part of an index
if (Kronos.scRT::right_format(
file_path = variables_binning$blacklist,
columns_to_check = 3,
logical = T
)) {
output$Blacklist_binning_out <-
shiny::renderText(variables_binning$blacklist)
variables_binning$activate_start5 = T
} else{
output$Blacklist_binning_out <-
shiny::renderText(
paste(
'<b><p style="color:#FF0000";> selected file does not have the required format.</b></p>'
)
)
variables_binning$activate_start5 = F
}
} else{
output$Blacklist_binning_out <-
shiny::renderText(NULL)
variables_binning$activate_start5 = T
variables_binning$blacklist = NULL
}
})
##activate start
shiny::observeEvent(
c(
variables_binning$activate_start1,
variables_binning$activate_start2,
variables_binning$activate_start3,
variables_binning$activate_start4,
variables_binning$activate_start5
),
{
if (variables_binning$activate_start1 &
variables_binning$activate_start2 &
variables_binning$activate_start3 &
variables_binning$activate_start4 &
variables_binning$activate_start5)
{
shinyjs::enable('run_binning')
} else
{
shinyjs::disable('run_binning')
}
}
)
#manual parameters change
shiny::observeEvent(input$Reads_type_binning, {
variables_binning$read_type = input$Reads_type_binning
})
shiny::observeEvent(input$Read_size_binning, {
variables_binning$read_size = input$Read_size_binning
})
shiny::observeEvent(input$Fragment_size_binning, {
variables_binning$frag_size = input$Fragment_size_binning
})
#run
shiny::observeEvent(input$run_binning, {
if (input$run_binning > 0) {
#disable buttons
shinyjs::disable('RefGenome_binning')
shinyjs::disable('index_binning')
shinyjs::disable('out_binning')
shinyjs::disable('Param_binning')
shinyjs::disable('Bam_binning')
shinyjs::disable('Coverage_binning')
shinyjs::disable('Reads_type_binning')
shinyjs::disable('Read_size_binning')
shinyjs::disable('Fragment_size_binning')
shinyjs::disable('Cores_binning')
shinyjs::disable('Mappability_binning')
shinyjs::disable('ErrorRate_binning')
shinyjs::disable('Blacklist_binning')
shinyjs::disable('chr_prefix_binning')
shinyjs::disable('chr_range_binning')
shinyjs::disable('BinSize_binning')
shinyjs::disable('run_binning')
#start binning
bins = Kronos.scRT::binning(
RefGenome = variables_binning$fasta,
bowtie2_index = variables_binning$index,
bin_size = input$BinSize_binning * 1000,
read_size = variables_binning$read_size,
fragment_size = variables_binning$frag_size,
paired_ends = variables_binning$read_type == 'PE',
directory_to_bamfiles = variables_binning$Bam_dir,
tmp_dir = file.path(variables_binning$out, 'tmp'),
upper_mappability_th = max(input$Mappability_binning),
lower_mappability_th = min(input$Mappability_binning),
black_list = variables_binning$blacklist,
coverage = input$Coverage_binning,
errorRate = input$ErrorRate_binning / 100,
cores = input$Cores_binning,
chr_prefix = ifelse(
input$chr_prefix_binning == '',
NULL,
input$chr_prefix_binning
),
chr_range = input$chr_range_binning,
return_estimated_param = T
)
#if directory_to_bamfiles is given return parameters
param = bins$param
bins = bins$bins
#write file
readr::write_tsv(bins, file.path(
variables_binning$out,
paste0(
basename(variables_binning$index),
'_',
input$BinSize_binning,
'kb_bins_coverage_',
input$Coverage_binning,
'X_',
paste0(
'reads_',
param$read_size,
'bp_',
ifelse(
param$paired_ends,
paste0('PE_fragmentSize_', param$fragment_size, 'bp_')
,
'SE_'
)
),
ifelse(
!is.null(variables_binning$blacklist),
'blacklisted_',
''
),
paste0(
'error_rate_',
input$ErrorRate_binning,
'_min_mappability_',
min(input$Mappability_binning),
'_max_mappability_',
max(input$Mappability_binning)
),
'.tsv'
)
))
#enable
shinyjs::enable('RefGenome_binning')
shinyjs::enable('index_binning')
shinyjs::enable('out_binning')
shinyjs::enable('Param_binning')
shinyjs::enable('Bam_binning')
shinyjs::enable('Coverage_binning')
shinyjs::enable('Reads_type_binning')
shinyjs::enable('Read_size_binning')
shinyjs::enable('Fragment_size_binning')
shinyjs::enable('Cores_binning')
shinyjs::enable('Mappability_binning')
shinyjs::enable('ErrorRate_binning')
shinyjs::enable('Blacklist_binning')
shinyjs::enable('chr_prefix_binning')
shinyjs::enable('chr_range_binning')
shinyjs::enable('run_binning')
shinyjs::enable('BinSize_binning')
}
})
}
#### CN
{
#set shiny Files buttons
shinyFiles::shinyDirChoose(
input = input,
id = 'Bamdir_CN',
session = session,
roots = roots,
defaultRoot = 'Home'
)
shinyFiles::shinyDirChoose(
input = input,
id = 'Output_CN',
session = session,
roots = roots,
defaultRoot = 'Home'
)
shinyFiles::shinyFileChoose(
input = input,
id = 'Bins_CN',
session = session,
roots = roots,
defaultRoot = 'Home'
)
shinyFiles::shinyFileChoose(
input = input,
id = 'ChrSize_CN',
session = session,
roots = roots,
defaultRoot = 'Home'
)
#set variables
variables_cn = reactiveValues(
Bamdir_CN = NULL,
Output_CN = NULL,
Bins_CN = NULL,
ChrSize_CN = NULL,
Samples = dplyr::tibble(),
run_ok1 = F,
run_ok2 = F,
sample_counter = 0,
group_counter = 0
)
# ui if user wants fix ploidy average
output$FixAveragePloidy = shiny::renderUI({
shiny::req(input$Ploidy_Restrictions_CN == 'Fix Average Ploidy')
shiny::fluidRow(shiny::column(
width = 3,
shiny::numericInput(
inputId = 'meanPloidy_CN',
label = 'Average ploidy',
value = 2,
min = 1,
step = 0.1,
width = '100%'
)
))
})
# ui if user wants fix ploidy average
output$FixPloidyRange = shiny::renderUI({
shiny::req(input$Ploidy_Restrictions_CN == 'Fix Ploidy Range')
shiny::fluidRow(
shiny::column(
width = 3,
shiny::numericInput(
inputId = 'minPloidy_CN',
label = 'Min accepted ploidy',
value = 2,
min = 0,
step = 0.1,
width = '100%'
)
),
shiny::column(
width = 3,
shiny::numericInput(
inputId = 'maxPloidy_CN',
label = 'Max accepted ploidy',
value = 8,
min = 0,
step = 0.1,
width = '100%'
)
)
)
})
#set output folder
shiny::observeEvent(input$Output_CN, {
if (!is.numeric(input$Output_CN)) {
variables_cn$Output_CN = shinyFiles::parseDirPath(roots = roots, selection = input$Output_CN)
} else{
variables_cn$Output_CN = NULL
}
output$Output_CN = shiny::renderText(variables_cn$Output_CN)
})
#set BinsFile
shiny::observeEvent(input$Bins_CN, {
if (!is.numeric(input$Bins_CN)) {
variables_cn$Bins_CN = shinyFiles::parseFilePaths(roots = roots, selection = input$Bins_CN)
variables_cn$Bins_CN = variables_cn$Bins_CN$datapath
variables_cn$Bins_CN = Kronos.scRT::right_format(
file_path = variables_cn$Bins_CN,
columns_to_check = c(
'chr',
'start',
'end',
'mappability',
'mappability_th',
'gc_frequency',
'type'
),
wrong_message = paste(
'<b><p style="color:#FF0000";>',
variables_cn$Bins_CN,
'does not have the right format!</p></b>'
),
rigth_message = variables_cn$Bins_CN
)
} else{
variables_cn$Bins_CN = NULL
}
output$Bins_CN = shiny::renderText(variables_cn$Bins_CN)
})
#authorize run if binsfile is good
shiny::observeEvent(variables_cn$Bins_CN, {
if (!is.null(variables_cn$Bins_CN) &
stringr::str_detect(string = variables_cn$Bins_CN,
pattern = 'does not have the right format!</p></b>',
negate = T)) {
variables_cn$run_ok1 = T
} else{
variables_cn$run_ok1 = F
}
})
#set Chrsize
shiny::observeEvent(input$ChrSize_CN, {
if (!is.numeric(input$ChrSize_CN)) {
variables_cn$ChrSize_CN = shinyFiles::parseFilePaths(roots = roots, selection = input$ChrSize_CN)
variables_cn$ChrSize_CN = variables_cn$ChrSize_CN$datapath
variables_cn$ChrSize_CN = Kronos.scRT::right_format(
file_path = variables_cn$ChrSize_CN,
columns_to_check = c('chr',
'size'),
wrong_message = paste(
'<b><p style="color:#FF0000";>',
variables_cn$ChrSize_CN,
'does not have the right format!</p></b>'
),
rigth_message = variables_cn$ChrSize_CN
)
} else{
variables_cn$ChrSize_CN = NULL
}
output$ChrSize_CN = shiny::renderText(variables_cn$ChrSize_CN)
})
#authorize run if Chrsize is good
shiny::observeEvent(variables_cn$ChrSize_CN, {
if (!is.null(variables_cn$ChrSize_CN) &
stringr::str_detect(
string = variables_cn$ChrSize_CN,
pattern = 'does not have the right format!</p></b>',
negate = T
)) {
variables_cn$run_ok2 = T
} else{
variables_cn$run_ok2 = F
}
})
#set BAM folder
shiny::observeEvent(input$Bamdir_CN, {
if (!is.numeric(input$Bamdir_CN)) {
variables_cn$Bamdir_CN = shinyFiles::parseDirPath(roots = roots, selection = input$Bamdir_CN)
#check if file contains BAMS
if (!any(stringr::str_detect(
string = list.files(variables_cn$Bamdir_CN),
pattern = '.bam$'
))) {
variables_cn$Bamdir_CN = paste(
'<b><p style="color:#FF0000";>',
variables_cn$Bamdir_CN,
'does not contain bam files</p></b>'
)
shinyjs::disable('AddSample_CN')
} else{
shinyjs::enable('AddSample_CN')
}
} else{
variables_cn$Bamdir_CN = NULL
shinyjs::disable('AddSample_CN')
}
output$Bamdir_CN = shiny::renderText(variables_cn$Bamdir_CN)
})
#add samples
shiny::observeEvent(input$AddSample_CN, {
if (input$AddSample_CN > 0) {
shinyjs::disable('AddSample_CN')
variables_cn$Samples = rbind(
variables_cn$Samples,
dplyr::tibble(
Basename = input$basename_CN,
Group = input$group_CN,
Bamfiles = variables_cn$Bamdir_CN
)
)
output$Samples_CN = shiny::renderTable(variables_cn$Samples)
#reset interface
if (any(
stringr::str_detect(
string = variables_cn$Samples$Basename,
pattern = '^Exp_{0,1}[0-9]{0,3}$'
)
)) {
variables_cn$sample_counter = variables_cn$sample_counter + 1
shiny::updateTextInput(
inputId = 'basename_CN',
value = paste0('Exp_', variables_cn$sample_counter)
)
} else{
shinyjs::reset(input$basename_CN)
}
if (any(
stringr::str_detect(string = variables_cn$Samples$Group, pattern = '^Exp_{0,1}[0-9]{0,3}$')
)) {
variables_cn$group_counter = variables_cn$group_counter + 1
shiny::updateTextInput(
inputId = 'group_CN',
value = paste0('Exp_', variables_cn$group_counter)
)
} else{
shinyjs::reset(input$group_CN)
}
}
})
#activate run
shiny::observeEvent(
c(
variables_cn$Samples,
variables_cn$run_ok1,
variables_cn$run_ok2,
variables_cn$Output_CN
),
{
if (variables_cn$run_ok1 &
variables_cn$run_ok2 &
nrow(variables_cn$Samples) > 0 &
!is.null(variables_cn$Output_CN)) {
shinyjs::enable('Run_CN')
} else{
shinyjs::disable('Run_CN')
}
}
)
shiny::observeEvent(input$Run_CN, {
if (input$Run_CN > 0) {
#load df
Bins_CN = readr::read_tsv(variables_cn$Bins_CN)
ChrSize_CN = readr::read_tsv(variables_cn$ChrSize_CN)
shinyjs::disable('Run_CN')
for (i in 1:nrow(variables_cn$Samples)) {
if (input$Ploidy_Restrictions_CN != 'Fix Average Ploidy') {
results = Kronos.scRT::CallCNV(
directory = variables_cn$Samples$Bamfiles[i],
bins = Bins_CN,
chrom_size = ChrSize_CN,
basename = variables_cn$Samples$Basename[i],
group = variables_cn$Samples$Group[i],
tmp_dir = file.path(variables_cn$Output_CN, 'tmp'),
min_n_reads = input$min_reads_CN,
mim_mean_CN_accepted = ifelse(
is.null(input$minPloidy_CN),
2,
input$minPloidy_CN
),
max_mean_CN_accepted = ifelse(
is.null(input$maxPloidy_CN),
8,
input$maxPloidy_CN
),
chr_prefix = input$CHR_CN,
chr_range = input$CHR_RANGE_CN,
cores = input$Cores_CN
)
} else{
results = Kronos.scRT::CallCNV(
directory = variables_cn$Samples$Bamfiles[i],
bins = Bins_CN,
chrom_size = ChrSize_CN,
basename = variables_cn$Samples$Basename[i],
group = variables_cn$Samples$Group[i],
tmp_dir = file.path(variables_cn$Output_CN, 'tmp'),
min_n_reads = input$min_reads_CN,
ploidy = ifelse(
is.null(input$meanPloidy_CN),
2,
input$meanPloidy_CN
),
chr_prefix = input$CHR_CN,
chr_range = input$CHR_RANGE_CN,
cores = input$Cores_CN
)
}
dir = file.path(variables_cn$Output_CN,
variables_cn$Samples$Basename[i])
if (!dir.exists(dir)) {
dir.create(dir)
}
results$PerCell %>%
readr::write_csv(file = file.path(
dir,
paste0(variables_cn$Samples$Basename[i], '_PerCell.csv')
))
results$CNV %>%
readr::write_tsv(file = file.path(
dir,
paste0(variables_cn$Samples$Basename[i], '_scCNV.tsv')
))
}
}
})
}
}
# Run the application
shiny::shinyApp(ui = ui,
server = server)
CL-CHEN-Lab/User_interface_for_Kronos_scRT documentation built on Aug. 1, 2022, 2:08 p.m.
R Package Documentation
Browse R Packages
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
#options
options(stringsAsFactors = FALSE,
dplyr.summarise.inform=FALSE,
warn = 1,
scipen = 999)
#load operator
`%>%` = tidyr::`%>%`
#set ggplot theme
ggplot2::theme_set(new = ggplot2::theme_bw())
#Java function to close this app
jscode <- "shinyjs.closeWindow = function() { window.close(); }"
#find max number of cores
maxCores = parallel::detectCores()
# Define UI
ui <- shinydashboard::dashboardPage(
title = 'Kronos scRT',
skin = 'red',
shinydashboard::dashboardHeader(title = shiny::span(
shiny::img(src = 'KronosLogo.png', width = '100%')
)),
shinydashboard::dashboardSidebar(
shinydashboard::sidebarMenu(
id = 'Sidebar',
shinydashboard::menuItem(text = "FastqToBam",
tabName = "Home"),
shinydashboard::menuItem(text = "FastqToBam Metrics",
tabName = "Metrics"),
shinydashboard::menuItem(text = "Binning",
tabName = "Binning"),
shinydashboard::menuItem(text = "Copy Number Calling",
tabName = "CN"),
shinydashboard::menuItem(text = "10XGenomics data conversion",
tabName = "10X"),
shinydashboard::menuItem(text = "Exit",
tabName = "Exit")
)
),
shinydashboard::dashboardBody(
#use shinyjs
shinyjs::useShinyjs(),
#to close window
shinyjs::extendShinyjs(text = jscode, functions = c("closeWindow")),
#use CSS
shiny::tags$head(
shiny::tags$link(rel = "stylesheet",
type = "text/css",
href = "custom.css")
),
#setting spinner
shinybusy::add_busy_spinner(
spin = "fading-circle",
position = 'bottom-right',
color = 'red',
height = '200px',
width = '200px'
),
shinydashboard::tabItems(#####home
{
shinydashboard::tabItem(tabName = "Home",
shiny::fluidPage(
shiny::fluidRow(
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyDirButton(
id = 'Fastq',
label = 'Fastq files folder',
title = 'Fastq files folder',
style = 'width:100%;'
)
),
shiny::column(width = 9, shiny::htmlOutput('Fastq_out'))
),
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyFilesButton(
id = 'index',
label = shiny::div(
'Bowtie2 index',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = "Select one of the index files. If you don't have a compiled index, you can download one from http://bowtie-bio.sourceforge.net/bowtie2." , placement = 'right')
),
title = 'Bowtie2 index',
style = 'width:100%;',
multiple = F
)
),
shiny::column(width = 9, shiny::htmlOutput('index_out'))
),
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyFilesButton(
id = 'Adapters',
label = shiny::div(
'Adapters list',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'A text files with one adapter per line with no header. If not provided Kronos will look for standard illumina adapters' , placement = 'right')
),
title = 'Adapters list',
style = 'width:100%;',
multiple = F
)
),
shiny::column(width = 9, shiny::htmlOutput('Adapters_out'))
),
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyDirButton(
id = 'out',
label = 'Output files folder',
title = 'Output files folder',
style = 'width:100%;'
)
),
shiny::column(width = 9, shiny::htmlOutput('Output_out'))
),
shiny::fluidRow(
shiny::column(
width = 3,
shiny::radioButtons(
inputId = 'reads_type',
label = 'Sequencing',
choices = c('PE', 'SE', 'PE to treat as SE'),
inline = T,
selected = 'PE',
width = '100%'
)
),
shiny::column(
width = 3,
shiny::numericInput(
inputId = 'min_size',
label = 'Read min size after trimming',
value = 25,
min = 15,
step = 1,
width = '100%'
)
),
shiny::column(
width = 3,
shiny::radioButtons(
inputId = 'phred33',
label = 'Quality score',
choiceValues = c(T, F) ,
choiceNames = c('phred33', 'phred64'),
selected = T,
inline = T,
width = '100%'
)
)
),
shiny::uiOutput('patter_sample'),
shiny::fluidRow(shiny::column(
width = 3,
shiny::sliderInput(
inputId = 'cores',
label = 'Cores to use',
min = 1,
max = maxCores,
value = trunc(maxCores / 2),
step = 1
)
)),
shiny::fluidRow(shiny::column(
width = 3,
shinyjs::disabled(
shiny::actionButton(
inputId = 'run',
label = 'Run',
width = '100%'
)
)
)),
shiny::fluidRow(shiny::column(width = 12,
shiny::htmlOutput('final')))
)
))
},
######metrics
{
shinydashboard::tabItem(
tabName = "Metrics",
shiny::fluidRow(
shiny::column(
width = 4,
align = 'center',
shinyFiles::shinyFilesButton(
id = 'Load_metrics',
label = 'Load old Metrics',
title = 'Load old Metrics',
multiple = F,
style = 'width:75%;'
)
),
shiny::column(
width = 4,
align = 'center',
shinyjs::disabled(
shinyFiles::shinySaveButton(
id = 'Save_plots',
label = 'Save diagnostic plot',
title = 'Save diagnostic plot',
filetype = '.pdf',
style = 'width:75%;'
)
)
),
shiny::column(
width = 4,
align = 'center',
shinyjs::disabled(
shinyFiles::shinySaveButton(
id = 'Save_table',
label = 'Save table',
title = 'Save table',
filetype = '.tsv',
style = 'width:75%;'
)
)
)
),
shiny::fluidRow(shiny::column(
width = 12,
shiny::plotOutput(
'final_plot1',
# click = shiny::clickOpts(id = 'final_plot_click1'),
brush = shiny::brushOpts(id = 'final_plot_brush1',
resetOnNew = T),
dblclick = shiny::dblclickOpts(id = 'final_plot_dclick1', clip = T, delay = 200)
)
)),
shiny::fluidRow(shiny::column(
width = 12,
shinyjs::hidden(
shiny::radioButtons(
inputId = 'final_table_selector',
label = 'Parameter',
choices = '',
inline = F,
width = '100%'
)
)
)),
shiny::fluidRow(shiny::column(
width = 12,
shiny::tableOutput('final_table')
))
)
},
#####binning
{
shinydashboard::tabItem(
tabName = "Binning",
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyFilesButton(
id = 'RefGenome_binning',
label = shiny::div(
'Reference genome fasta file',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = "For most genomes, fasta file can be downloaded from UCSC Genome Browser. N.B. you need to download the file containing all chromosomes." , placement = 'right')
),
title = 'Reference genome fasta file',
multiple = F,
style = 'width:100%;'
)
),
shiny::column(width = 9,
shiny::htmlOutput('RefGenome_binning_out'))
),
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyFilesButton(
id = 'index_binning',
label = shiny::div(
'Bowtie2 index',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = "Select one of the index files. If you don't have a compiled index, you can download one from http://bowtie-bio.sourceforge.net/bowtie2." , placement = 'right')
),
title = 'Bowtie2 index',
style = 'width:100%;',
multiple = F
)
),
shiny::column(width = 9, shiny::htmlOutput('index_binning_out'))
),
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyDirButton(
id = 'out_binning',
label = 'Output files folder',
title = 'Output files folder',
style = 'width:100%;'
)
),
shiny::column(width = 9, shiny::htmlOutput('Output_binning_out'))
),
shiny::fluidRow(
shiny::column(
width = 3,
shiny::radioButtons(
inputId = 'Param_binning',
label = 'Parameters estimation',
choices = c('Auto', 'Manual'),
selected = 'Auto',
inline = T,
width = '100%'
)
)),
shiny::uiOutput('Paramui_binning_out1'),
shiny::uiOutput('Paramui_binning_out2'),
shiny::fluidRow(
shiny::column(
width = 3,
shiny::sliderInput(
inputId = 'Coverage_binning',
label = shiny::div(
'Coverage',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'Simulated dept of sequencing to calculate bin mappability.' , placement = 'right')
),
min = 1,
max = 10,
value = 1,
step = 1,
post = 'X',
width = '100%'
)
),
shiny::column(
width = 3,
shiny::sliderInput(
inputId = 'BinSize_binning',
label = shiny::div(
'BinSize',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'Bin size that will be used to call CNV. This size does not correspond to the final scRT resolution. The bin size should increased if the average cell coverage is very low.' , placement = 'right')
),
min = 5,
max = 100,
value = 20,
step = 1,
post = 'kb',
width = '100%'
)
),
shiny::column(
width = 3,
shiny::sliderInput(
inputId = 'Cores_binning',
label = 'Cores',
min = 1,
max = maxCores,
value = trunc(maxCores / 2),
step = 1,
width = '100%'
)
)
),
shinydashboard::box(
title = 'Advanced options',
status = 'primary',
solidHeader = T,
width = '100%',
collapsible = T,
collapsed = T,
shiny::fluidRow(
shiny::column(
width = 3,
shiny::sliderInput(
inputId = 'Mappability_binning',
label = shiny::div(
'Acceptable mappability range',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'Bins with mappability higher or lower than the acceptable mappability range will be excluded from the analysis.' , placement = 'right')
),
min = 0.5,
max = 3,
value = c(0.8, 1.5),
step = 0.1,
width = '100%'
)
),
shiny::column(
width = 3,
shiny::sliderInput(
inputId = 'ErrorRate_binning',
label = shiny::div(
'Sequencer Error Rate',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'Is the error rate of the sequencer you used to sequence your data. This parameter is used to simulates reads and calculate the bin mappability.' , placement = 'right')
),
min = 0,
max = 0.3,
value = 0.1,
post = '%',
step = 0.001,
width = '100%'
)
)
),
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyFilesButton(
id = 'Blacklist_binning',
label = shiny::div(
'Blacklist',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'Because of their repetitive nature, some regions of the genome are difficult to map. The user can hide these regions form the analysis providing a blacklist file. Such lists are available in literature. Some useful ones can be found at https://github.com/Boyle-Lab/Blacklist' , placement = 'right')
),
title = 'Blacklist',
multiple = F
)
),
shiny::column(width = 9,
shiny::htmlOutput('Blacklist_binning_out'))
)
),
shiny::fluidRow(
shiny::column(
width = 3,
shiny::textInput(
inputId = 'chr_prefix_binning',
label = shiny::div(
'Chromosome prefix',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'Depending on your reference genome, chromosomes or scaffolds could be named differently. Please, provide the prefix that precedes the chromosome or scaffold number. If no prefix is present this box has to be emptied.' , placement = 'right')),
value = 'chr',
width = '100%'
)
),
shiny::column(
width = 3,
shiny::textInput(
inputId = 'chr_range_binning',
label = shiny::div(
'Chromosomes to consider',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'Chromosome to include in the analysis. You can define ranges using ":" and individual chromosomes using ",". Don\'t include the chr prefix!' , placement = 'right')
),
value = '1:22',
width = '100%'
)
)
),
shiny::fluidRow(shiny::column(
width = 3,
shinyjs::disabled(
shiny::actionButton(
inputId = 'run_binning',
label = 'Run',
width = '100%'
)
)
))
)
},
#####CN
{
shinydashboard::tabItem(
tabName = "CN",
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyFilesButton(
id = 'Bins_CN',
label = div('Bins file',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'Bins file created during the binning step.' , placement = 'right')),
title = 'Bins file',
style = 'width:100%;',
multiple = F
)
),
shiny::column(width = 9,
shiny::htmlOutput('Bins_CN'))
),
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyFilesButton(
id = 'ChrSize_CN',
label = shiny::div(
'Chrom size file',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'For most genome assemblies this file can be downloaded from UCSC Genome Browser website.' , placement = 'right')),
title = 'Chrom size file',
style = 'width:100%;',
multiple = F
)
),
shiny::column(width = 9,
shiny::htmlOutput('ChrSize_CN'))
),
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyDirButton(
id = 'Output_CN',
label = 'Results folder',
title = 'Results folder',
style = 'width:100%;'
)
),
shiny::column(width = 9,
shiny::htmlOutput('Output_CN'))
),
shiny::fluidRow(
shiny::column(
width = 3,
shiny::textInput(
inputId = 'CHR_CN',
label = shiny::div('Chromosome prefix',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'Depending on your reference genome, chromosomes or scaffolds could be named differently. Please, provide the prefix that precedes the chromosome or scaffold number. If no prefix is present this box has to be emptied.' , placement = 'right')
),
value = 'chr',
width = '100%'
)
),
shiny::column(
width = 3,
shiny::textInput(
inputId = 'CHR_RANGE_CN',
label = shiny::div(
'Chromosomes to consider',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'Chromosome to include in the analysis. You can define ranges using ":" and individual chromosomes using ",". Don\'t include the chr prefix!' , placement = 'right')
),
value = '1:22',
width = '100%'
)
),
shiny::column(
width = 3,
shiny::sliderInput(
inputId = 'Cores_CN',
label = 'Number of cores',
min = 1,
max = maxCores,
value = trunc(maxCores / 2),
step = 1
)
)
),
shinydashboard::box(
title = 'Advanced options',
status = 'primary',
solidHeader = T,
width = 12,
collapsible = T,
collapsed = T,
shiny::fluidRow(shiny::column(
width = 3,
shiny::numericInput(
inputId = 'min_reads_CN',
label = shiny::div('Min number of reads per cell',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'This threshold depends on the genome size of your cells and on the chromosomes you want to keep in the analysis.' , placement = 'right')
),
value = 2 * 10 ^ 5,
step = 10 ^ 4,
width = '100%'
)
)),
shiny::fluidRow(shiny::column(
width = 12,
shiny::radioButtons(
inputId = 'Ploidy_Restrictions_CN',
label = div('Ploidy restrictions',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'If Fix Ploidy Range is selected, the software selects the most appropriated ploidy in the range and calculates the associated confidence. If Fix Average Ploidy is selected, cells are imposed the closest possible ploidy to the average one and does not calculate the confidence of this calling.' , placement = 'right')
),
choices = c('Fix Average Ploidy', 'Fix Ploidy Range'),
inline = T,
selected = 'Fix Ploidy Range',
width = '100%'
)
)),
shiny::uiOutput('FixAveragePloidy'),
shiny::uiOutput('FixPloidyRange')
),
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyDirButton(
id = 'Bamdir_CN',
label = 'Bam files folder',
title = 'Bam files folder',
style = 'width:100%;'
)
),
column(width = 9,
shiny::htmlOutput('Bamdir_CN'))
),
shiny::fluidRow(
shiny::column(
width = 3,
shiny::textInput(
inputId = 'basename_CN',
label = shiny::div('Sample basename',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'This Name identifies each individual experiment. It can be modified later on in the analysis.' , placement = 'right')),
value = 'Exp',
width = '100%'
)
),
shiny::column(
width = 3,
shiny::textInput(
inputId = 'group_CN',
label = shiny::div('Sample group',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = 'If cells have been sequenced in different experiments, providing the same group name allows to merge them after normalization. It can be modified later on in the analysis.' , placement = 'right')),
value = 'Exp',
width = '100%'
)
)
),
shiny::fluidRow(shiny::column(
width = 3,
shinyjs::disabled(
shiny::actionButton(
inputId = 'AddSample_CN',
label = 'Add Sample',
width = '100%'
)
)
)),
shiny::fluidRow(shiny::column(
width = 9,
shiny::tableOutput('Samples_CN')
)),
shiny::fluidRow(shiny::column(
width = 3,
shinyjs::disabled(
shiny::actionButton(
inputId = 'Run_CN',
label = 'Run',
width = '100%'
)
)
))
)
},
#####10X
{
shinydashboard::tabItem(
tabName = "10X",
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyFilesButton(
id = 'PerCell_10X',
label = div('PerCell',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = '10XGenomics per_cell_summary_metrics.csv' , placement = 'right')),
title = 'PerCell file',
style = 'width:100%;',
multiple = F
)
),
shiny::column(width = 9,
shiny::htmlOutput('PerCell_10X'))
),
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyFilesButton(
id = 'CNV_10X',
label = shiny::div(
'CNV',
bsplus::shiny_iconlink() %>%
bsplus::bs_embed_popover(title = '10XGenomics node_cnv_calls.bed' , placement = 'right')),
title = 'CNV_10X',
style = 'width:100%;',
multiple = F
)
),
shiny::column(width = 9,
shiny::htmlOutput('CNV_10X'))
),
shiny::fluidRow(
shiny::column(
width = 3,
shiny::textInput(
inputId = 'Basename_10X',
label = 'Basename',
value = 'Exp',
width = '100%'
)
),
shiny::column(
width = 3,
shiny::textInput(
inputId = 'Group_10X',
label = 'Group',
value = 'Exp',
width = '100%'
)
)),
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyDirButton(
id = 'Output_10X',
label = 'Results folder',
title = 'Results folder',
style = 'width:100%;'
)
),
shiny::column(width = 9,
shiny::htmlOutput('Output_10X'))
),
shiny::fluidRow(
shiny::column(
width = 3,
shinyjs::disabled(
shiny::actionButton(inputId = 'Run_10X',label = 'Run',width = '100%'))
)
)
)
})
)
)
server <- function(input, output, session) {
#define operators
`%>%` = tidyr::`%>%`
`%do%` = foreach::`%do%`
`%dopar%` = foreach::`%dopar%`
#find max number of cores
maxCores = parallel::detectCores()
#set roots
roots = c(shinyFiles::getVolumes()(),
Home = Sys.getenv("HOME"))
#set shinyFiles buttons
shinyFiles::shinyDirChoose(
input = input,
id = 'Fastq',
session = session,
roots = roots,
defaultRoot = 'Home'
)
shinyFiles::shinyDirChoose(
input = input,
id = 'out',
session = session,
roots = roots,
defaultRoot = 'Home'
)
shinyFiles::shinyFileChoose(
input = input,
id = 'index',
session = session,
roots = roots,
defaultRoot = 'Home'
)
shinyFiles::shinyFileChoose(
input = input,
id = 'Adapters',
session = session,
roots = roots,
defaultRoot = 'Home'
)
shinyFiles::shinyFileChoose(
input = input,
id = 'fasta',
session = session,
roots = roots,
defaultRoot = 'Home'
)
shinyFiles::shinyDirChoose(
input = input,
id = 'Output_10X',
session = session,
roots = roots,
defaultRoot = 'Home'
)
shinyFiles::shinyFileChoose(
input = input,
id = 'CNV_10X',
session = session,
roots = roots,
defaultRoot = 'Home'
)
shinyFiles::shinyFileChoose(
input = input,
id = 'PerCell_10X',
session = session,
roots = roots,
defaultRoot = 'Home'
)
#define variables
variables = reactiveValues(
File1 = NULL,
File2 = NULL,
Adapters = NULL,
out = NULL,
fastq_dir = NULL,
index = NULL,
activate_start1 = F,
activate_start2 = F,
activate_start3 = F,
proceed_run = F,
info = dplyr::tibble()
)
variables_binning = reactiveValues(
fasta = NULL,
index = NULL,
out = NULL,
Bam_dir = NULL,
blacklist = NULL,
activate_start1 = F,
activate_start2 = F,
activate_start3 = F,
activate_start4 = F,
activate_start5 = T,
read_size = 40,
frag_size = 200,
read_type = 'PE'
)
variables_10X = reactiveValues(
Output_10X=NULL,
PerCell_10X=NULL,
CNV_10X=NULL,
)
###10X to Kronos
{
#set output folder
shiny::observeEvent(input$Output_10X, {
if (!is.numeric(input$Output_10X)) {
variables_10X$Output_10X = shinyFiles::parseDirPath(roots = roots, selection = input$Output_10X)
} else{
variables_10X$Output_10X = NULL
}
output$Output_10X = shiny::renderText(variables_10X$Output_10X)
})
#set PerCell_10X
shiny::observeEvent(input$PerCell_10X, {
if (!is.numeric(input$PerCell_10X)) {
variables_10X$PerCell_10X = shinyFiles::parseFilePaths(roots = roots, selection = input$PerCell_10X)
variables_10X$PerCell_10X = variables_10X$PerCell_10X$datapath
variables_10X$PerCell_10X = Kronos.scRT::right_format(
file_path = variables_10X$PerCell_10X,
delim = ',',
columns_to_check = c(
"barcode",
"cell_id",
"total_num_reads",
"num_unmapped_reads" ,
"num_lowmapq_reads",
"num_duplicate_reads" ,
"num_mapped_dedup_reads",
"frac_mapped_duplicates",
"effective_depth_of_coverage",
"effective_reads_per_1Mbp" ,
"raw_mapd",
"normalized_mapd" ,
"raw_dimapd",
"normalized_dimapd" ,
"mean_ploidy",
"ploidy_confidence" ,
"is_high_dimapd",
"is_noisy"
),
wrong_message = paste(
'<b><p style="color:#FF0000";>',
variables_10X$PerCell_10X,
'does not have the right format!</p></b>'
),
rigth_message = variables_10X$PerCell_10X
)
} else{
variables_10X$PerCell_10X = NULL
}
output$PerCell_10X = shiny::renderText(variables_10X$PerCell_10X)
})
#set CN_10X
shiny::observeEvent(input$CNV_10X, {
if (!is.numeric(input$CNV_10X)) {
variables_10X$CNV_10X = shinyFiles::parseFilePaths(roots = roots, selection = input$CNV_10X)
variables_10X$CNV_10X = variables_10X$CNV_10X$datapath
variables_10X$CNV_10X = Kronos.scRT::right_format(
file_path = variables_10X$CNV_10X,
delim = '\t',skip = 2,
columns_to_check = c(
"#chrom",
"start",
"end",
"id",
"copy_number",
"event_confidence"
),
wrong_message = paste(
'<b><p style="color:#FF0000";>',
variables_10X$CNV_10X,
'does not have the right format!</p></b>'
),
rigth_message = variables_10X$CNV_10X
)
} else{
variables_10X$CNV_10X = NULL
}
output$CNV_10X = shiny::renderText(variables_10X$CNV_10X)
})
#basename and group
shiny::observeEvent(input$Group_10X, {
shiny::updateTextInput(inputId = 'Group_10X',value = stringr::str_replace(string = input$Group_10X,pattern = ' ',replacement = '_'))
})
shiny::observeEvent(input$Basename_10X, {
shiny::updateTextInput(inputId = 'Basename_10X',value = stringr::str_replace(string = input$Basename_10X,pattern = ' ',replacement = '_'))
})
#allow to run if files are selected
shiny::observeEvent(c(
variables_10X$Output_10X,
variables_10X$PerCell_10X,
variables_10X$CNV_10X
),
{
if(!is.null(variables_10X$Output_10X) &
!is.null(variables_10X$PerCell_10X)&
!is.null(variables_10X$CNV_10X)){
shinyjs::enable('Run_10X')
}else{
shinyjs::disable('Run_10X')
}
})
#run conversion
shiny::observeEvent(input$Run_10X,{
results=Kronos.scRT::TenXtoKronos(PerCell = variables_10X$PerCell_10X,CNV =variables_10X$CNV_10X,basename = input$Basename_10X, input$Group_10X)
results$PerCell%>%
readr::write_csv(paste0(file.path(variables_10X$Output_10X, 'Kronos_format_'), basename(variables_10X$PerCell_10X)))
results$CNV%>%
readr::write_tsv(paste0(file.path(variables_10X$Output_10X, 'Kronos_format_'), stringr::str_replace(string = basename(variables_10X$CNV_10X),pattern = '.bed',replacement = '.tsv')))
shiny::updateTextInput(inputId = 'Group_10X',value = 'Exp')
shiny::updateTextInput(inputId = 'Basename_10X',value = 'Exp')
variables_10X$PerCell_10X=NULL
variables_10X$CNV_10X=NULL
output$CNV_10X = shiny::renderText(variables_10X$CNV_10X)
output$PerCell_10X = shiny::renderText(variables_10X$PerCell_10X)
})
}
##fastqToBam
{
#stop app when the session ends
session$onSessionEnded(function() {
shiny::stopApp()
})
#load tex input if PE format
shiny::observeEvent(input$reads_type, {
if (input$reads_type != 'SE') {
output$patter_sample = shiny::renderUI({
shiny::fluidRow(column(
width = 3,
shiny::textInput(
inputId = 'R1',
label = 'Pattern to identify R1 fastq',
value = '_R1'
)
),
column(
width = 3,
shiny::textInput(
inputId = 'R2',
label = 'Pattern to identify R2 fastq',
value = '_R2'
)
))
})
} else{
output$patter_sample = shiny::renderUI({
NULL
})
}
})
###select fastq folder
shiny::observeEvent(input$Fastq, {
output$final <- shiny::renderText(NULL)
if (!is.numeric(input$Fastq)) {
#recover fastq directory
variables$fastq_dir = shinyFiles::parseDirPath(selection = input$Fastq, roots = roots)
#check for fastq files
if (length(list.files(path = variables$fastq_dir, pattern = 'fastq|fq')) >
0) {
output$Fastq_out <- shiny::renderText(variables$fastq_dir)
variables$activate_start1 = T
} else{
output$Fastq_out <-
shiny::renderText(
paste(
'<b><p style="color:#FF0000";> selected directory does not contain fastq files</b></p>'
)
)
variables$activate_start1 = F
}
} else{
variables$activate_start1 = F
output$Fastq_out <- shiny::renderText(NULL)
}
})
###select index
shiny::observeEvent(input$index, {
output$final <- shiny::renderText(NULL)
if (!is.numeric(input$index)) {
#recover index directory
variables$index = shinyFiles::parseFilePaths(selection = input$index, roots = roots)
variables$index = variables$index$datapath
#check that the selected file is actually part of an index
if (stringr::str_detect(string = variables$index, pattern = '.bt2')) {
variables$index = stringr::str_remove(variables$index, pattern = '.[0-9]{1,2}.bt2|.rev.[0-9]{1,2}.bt2')
output$index_out <- shiny::renderText(variables$index)
variables$activate_start3 = T
} else{
output$index_out <-
shiny::renderText(
paste(
'<b><p style="color:#FF0000";> selected file does not belong to a bowtie2 index.</b></p>'
)
)
variables$activate_start3 = F
}
} else{
variables$activate_start3 = F
output$index_out <-
shiny::renderText(NULL)
}
})
###select adapter
shiny::observeEvent(input$Adapters,
{
if (!is.numeric(input$Adapters))
{
#recover index directory
variables$Adapters = shinyFiles::parseFilePaths(selection = input$Adapters, roots = roots)
variables$Adapters = variables$Adapters$datapath
#check that the selected file is actually part of an index
if (Kronos.scRT::right_format(
file_path = variables$Adapters,
columns_to_check = 1,
logical = T
)) {
variables$Adapters = readr::read_lines(variables$Adapters)
output$Adapters_out <-
shiny::renderText(variables$Adapters)
} else
{
output$Adapters_out <-
shiny::renderText(
paste(
'<b><p style="color:#FF0000";> Adapters file has to be a text file with one adapter per line, No header!</b></p>'
)
)
}
}
})
###select out folder
shiny::observeEvent(input$out,
{
output$final <- shiny::renderText(NULL)
if (!is.numeric(input$out))
{
#recover fastq directory
variables$out = shinyFiles::parseDirPath(selection = input$out, roots = roots)
#check for fastq files
if (length(list.files(path = variables$out)) == 0)
{
output$Output_out <- shiny::renderText(variables$out)
variables$activate_start2 = T
} else{
output$Output_out <-
shiny::renderText(
paste(
'<b><p style="color:#FF0000";> selected directory is not empty</b></p>'
)
)
variables$activate_start2 = F
}
} else{
variables$activate_start2 = F
output$Output_out <-
shiny::renderText(NULL)
}
})
##activate start
shiny::observeEvent(
c(
variables$activate_start1,
variables$activate_start2,
variables$activate_start3
),
{
if (variables$activate_start1 &
variables$activate_start2 &
variables$activate_start3)
{
shinyjs::enable('run')
} else
{
shinyjs::disable('run')
}
}
)
###start
shiny::observeEvent(input$run,
{
if (input$run > 0)
{
#disable all buttons till the end of the run
shinyjs::disable('run')
shinyjs::disable('Fastq')
shinyjs::disable('out')
shinyjs::disable('reads_type')
shinyjs::disable('cores')
shinyjs::disable('Adapters')
shinyjs::disable('index')
all_files = list.files(
path = variables$fastq_dir,
pattern = 'fastq|fq',
ignore.case = T,
full.names = T
)
if (input$reads_type == 'PE')
{
R1 = stringr::str_detect(string = basename(all_files),
pattern = input$R1)
R2 = stringr::str_detect(string = basename(all_files),
pattern = input$R2)
variables$File1 = all_files[R1]
variables$File2 = all_files[R2]
#check if file names order is matching
if (all(
stringr::str_split(
string = variables$File1,
pattern = input$R1,
simplify = T
)
[, 1] == stringr::str_split(
string = variables$File2,
pattern = input$R2,
simplify = T
)[, 1]
)) {
variables$proceed_run = T
} else
{
variables$proceed_run = F
}
} else
if (input$reads_type == 'SE')
{
variables$File1 = all_files
variables$proceed_run = T
} else
{
R1 = stringr::str_detect(string = all_files, pattern = input$R1)
R2 = stringr::str_detect(string = all_files, pattern = input$R2)
variables$File1 = all_files[R1]
variables$File2 = all_files[R2]
#check if file names order is matching
if (all(
stringr::str_split(
string = variables$File1,
pattern = input$R1,
simplify = T
)
[, 1] == stringr::str_split(
string = variables$File2,
pattern = input$R2,
simplify = T
)[, 1]
)) {
variables$proceed_run = T
cl = snow::makeCluster(input$cores)
doSNOW::registerDoSNOW(cl)
shiny::isolate({
file1 = variables$File1
file2 = variables$File2
out = variables$out
})
variables$File1 = foreach::foreach(i = 1:length(variables$File1)) %dopar%
{
Kronos.scRT::mergefastq(
FileList = c(file1[i], file2[i]),
output = file.path(out, 'MergedFastq')
)
}
snow::stopCluster(cl)
variables$File2 = NULL
variables$File1 = unlist(variables$File1)
variables$proceed_run = T
} else{
variables$proceed_run = F
}
}
if (variables$proceed_run) {
if (input$reads_type == 'PE') {
variables$info = Kronos.scRT::FastqToBam(
bowtie2_index = variables$index,
File1 = variables$File1,
File2 = variables$File2,
outputdir = variables$out,
adapters_list = variables$Adapters,
cores = input$cores,
Read_min_size_after_trimming = input$min_size,
phred33 = input$phred33
)
} else{
variables$info = Kronos.scRT::FastqToBam(
bowtie2_index = variables$index,
File1 = variables$File1,
outputdir = variables$out,
adapters_list = variables$Adapters,
cores = input$cores,
Read_min_size_after_trimming = input$min_size,
phred33 = input$phred33
)
}
#save info
variables$info %>% readr::write_tsv(file = file.path(variables$out, 'FastqToBamMetrics.tsv'))
shinydashboard::updateTabItems(session = session,
inputId = 'Sidebar',
selected = 'Metrics')
} else {
output$final_plot1 <-
shiny::renderPlot({
NULL
})
output$final_table <-
shiny::renderTable({
NULL
})
output$final <-
shiny::renderText(
'<b><p style="color:#FF0000";> files do not match, check your fastq folder.</b></p>'
)
}
#enable all buttons but run at the end of the run
shinyjs::enable('Fastq')
shinyjs::enable('out')
shinyjs::enable('reads_type')
shinyjs::enable('cores')
shinyjs::enable('Adapters')
shinyjs::enable('index')
}
})
####exit
{
shiny::observeEvent(input$Sidebar,
{
if (input$Sidebar == 'Exit') {
shinyjs::js$closeWindow()
shiny::stopApp()
}
})
}
}
####metrics
{
#shinyFiles buttons
shinyFiles::shinyFileSave(
input = input,
id = 'Save_plots',
session = session,
defaultRoot = 'Home',
roots = roots
)
shinyFiles::shinyFileSave(
input = input,
id = 'Save_table',
session = session,
defaultRoot = 'Home',
roots = roots
)
shinyFiles::shinyFileChoose(
input = input,
id = 'Load_metrics',
session = session,
defaultRoot = 'Home',
roots = roots
)
#upload data
shiny::observeEvent(input$Load_metrics, {
if (!is.numeric(input$Load_metrics)) {
#recover path and upload data
path = shinyFiles::parseFilePaths(roots = roots, selection = input$Load_metrics)
#check type
if (Kronos.scRT::right_format(
file_path = path$datapath,
columns_to_check = c('File', 'Parameter', 'Values', 'Category'),
logical = T
)) {
variables$Metrics = readr::read_tsv(path$datapath) %>%
dplyr::mutate(
Parameter = factor(Parameter, levels = unique(Parameter)),
Category = factor(Category, levels = unique(Category)),
x = ifelse(
Category %in% c('Total Reads', 'Unmapped Fraction', 'Proper Pair'),
1,
as.numeric(Category)
) + sample(
seq(-0.2, 0.2, 0.001),
size = dplyr::n(),
replace = T
)
) %>%
dplyr::ungroup()
#initialize Plot_selection
variables$Metrics$Color = 'red'
#active buttons
shinyjs::enable('Save_plots')
shinyjs::enable('Save_table')
#update select parameters
shiny::updateRadioButtons(
session = session,
inputId = 'final_table_selector',
choices = unique(variables$Metrics$Parameter),
inline = T
)
shinyjs::show('final_table_selector')
} else{
output$final_plot1 <- shiny::renderPlot(NULL)
output$final_table <- shiny::renderText('Wrong File!')
shinyjs::disable('Save_plots')
shinyjs::disable('Save_table')
shinyjs::hide('final_table_selector')
}
}
})
shiny::observeEvent(variables$info, {
if (nrow(variables$info) > 0) {
#add x variability for plotting
variables$Metrics = variables$info %>%
dplyr::mutate(
Category = factor(Category, levels = unique(Category)),
x = ifelse(
Category %in% c('Total Reads', 'Unmapped Fraction', 'Proper Pair'),
1,
as.numeric(Category)
) + sample(
seq(-0.2, 0.2, 0.001),
size = dplyr::n(),
replace = T
)
) %>%
dplyr::ungroup()
#initialise Plot_selection
variables$Metrics$Color = 'red'
#active buttons
shinyjs::enable('Save_plots')
shinyjs::enable('Save_table')
shiny::updateRadioButtons(
session = session,
inputId = 'final_table_selector',
choices = unique(variables$info$Parameter),
inline = T
)
shinyjs::show('final_table_selector')
}
})
#brush plot 1
shiny::observeEvent(input$final_plot_brush1, {
if (!is.null(input$final_plot_brush1)) {
#selected files
Files = variables$Metrics %>%
dplyr::filter(
Parameter == input$final_plot_brush1$panelvar1,
Values >= input$final_plot_brush1$ymin,
Values <= input$final_plot_brush1$ymax,
x >= input$final_plot_brush1$xmin,
x <= input$final_plot_brush1$xmax
) %>% dplyr::pull(File)
variables$Metrics = variables$Metrics %>%
dplyr::mutate(Color = ifelse(File %in% Files, 'red', 'black'))
}
})
#reset with dbclick
shiny::observeEvent(input$final_plot_dclick1,
{
#initialize reset
variables$Metrics = variables$Metrics %>%
dplyr::mutate(Color = 'red')
})
#if something has been selected
shiny::observeEvent(variables$Metrics, {
variables$plot1 = variables$Metrics %>%
dplyr::arrange(Color) %>%
ggplot2::ggplot() +
ggplot2::geom_boxplot(
ggplot2::aes(Category, Values),
outlier.size = 0,
outlier.colour = NA,
width = 0.8
) +
ggplot2::geom_point(ggplot2::aes(x, Values, color = Color), alpha =
0.5) +
ggplot2::theme_bw() +
ggplot2::labs(x = '', y = '') +
ggplot2::theme(
legend.position = 'none',
axis.text.x = ggplot2::element_text(
angle = 45,
hjust = 1,
vjust = 1
)
) +
ggplot2::scale_y_continuous(
labels = function(x)
sprintf(fmt = '%.1f', x)
) +
ggforce::facet_row(
~ Parameter,
scales = 'free',
space = 'free',
strip.position = 'right'
) +
ggplot2::scale_color_manual(values = c('red' = 'red', 'black', 'black'))
output$final_plot1 <-
shiny::renderPlot({
variables$plot1
})
})
shiny::observeEvent(c(variables$Metrics, input$final_table_selector), {
if (input$final_table_selector != '') {
output$final_table <-
shiny::renderTable(
variables$Metrics %>%
dplyr::filter(Parameter == input$final_table_selector,
Color == 'red') %>%
dplyr::select(-x, -Color) %>%
tidyr::spread(Category, Values)
)
}
})
##save
shiny::observeEvent(input$Save_plots, {
if (!is.numeric(input$Save_plots)) {
path = shinyFiles::parseSavePath(roots = roots, selection = input$Save_plots)
ggplot2::ggsave(
filename = path$datapath,
plot = variables$plot1,
device = grDevices::cairo_pdf,
width = 12,
height = 5
)
}
})
shiny::observeEvent(input$Save_table, {
if (!is.numeric(input$Save_table)) {
path = shinyFiles::parseSavePath(roots = roots, selection = input$Save_table)
variables$Metrics %>%
dplyr::select(-x, -Color) %>%
readr::write_tsv(file = path$datapath)
}
})
}
### Binning
{
#ui for auto selection of parameters
output$Paramui_binning_out1 = shiny::renderUI({
shiny::req(input$Param_binning == 'Auto')
shiny::fluidRow(
shiny::column(
width = 3,
shinyFiles::shinyDirButton(
id = 'Bam_binning',
label = 'Bam Files directory',
title = 'Bam Files directory',
style = 'width:100%;'
)
),
shiny::column(width = 6,
shiny::htmlOutput('Bam_binning_out'))
)
})
#ui for auto selection of parameters
output$Paramui_binning_out2 = shiny::renderUI({
shiny::req(input$Param_binning == 'Manual')
shiny::fluidRow(
shiny::column(
width = 3,
shiny::radioButtons(
inputId = 'Reads_type_binning',
label = 'Reads type',
choices = c('PE', 'SE'),
selected = variables_binning$read_type,
inline = T,
width = '100%'
)
),
shiny::column(
width = 3,
shiny::sliderInput(
inputId = 'Read_size_binning',
label = 'Read size',
min = 20,
max = 300,
value = variables_binning$read_size,
step = 1,
width = '100%'
)
),
shiny::column(width = 3,
shiny::uiOutput('Reads_type_binning'))
)
})
output$Reads_type_binning = shiny::renderUI({
shiny::req(input$Reads_type_binning == 'PE')
shiny::sliderInput(
inputId = 'Fragment_size_binning',
label = 'Fragment size',
min = 0,
max = 1000,
value = variables_binning$frag_size,
step = 1,
width = '100%'
)
})
#set shinyfiles
shinyFiles::shinyDirChoose(
input = input,
id = 'Bam_binning',
session = session,
roots = roots,
defaultRoot = 'Home'
)
shinyFiles::shinyFileChoose(
input = input,
id = 'RefGenome_binning',
session = session,
roots = roots,
defaultRoot = 'Home'
)
shinyFiles::shinyFileChoose(
input = input,
id = 'index_binning',
session = session,
roots = roots,
defaultRoot = 'Home'
)
shinyFiles::shinyDirChoose(
input = input,
id = 'out_binning',
session = session,
roots = roots,
defaultRoot = 'Home'
)
shinyFiles::shinyFileChoose(
input = input,
id = 'Blacklist_binning',
session = session,
roots = roots,
defaultRoot = 'Home'
)
# if manual setting is put on SE hide fragment size
shiny::observeEvent(input$Reads_type_binning, {
if (input$Reads_type_binning == 'SE') {
shinyjs::hide('Fragment_size_binning')
} else{
shinyjs::show('Fragment_size_binning')
}
})
#select fasta file
shiny::observeEvent(input$RefGenome_binning, {
if (!is.numeric(input$RefGenome_binning)) {
#recover path
variables_binning$fasta = shinyFiles::parseFilePaths(roots = roots,
selection = input$RefGenome_binning)
variables_binning$fasta = variables_binning$fasta$datapath
output$RefGenome_binning_out = shiny::renderText({
variables_binning$fasta
})
# first step to activate run
variables_binning$activate_start1 = T
} else{
variables_binning$fasta = NULL
output$RefGenome_binning_out = shiny::renderText({
variables_binning$fasta
})
variables_binning$activate_start1 = F
}
})
###select index
shiny::observeEvent(input$index_binning, {
if (!is.numeric(input$index_binning)) {
#recover index directory
variables_binning$index = shinyFiles::parseFilePaths(selection = input$index_binning,
roots = roots)
variables_binning$index = variables_binning$index$datapath
#check that the selected file is actually part of an index
if (stringr::str_detect(string = variables_binning$index, pattern = '.bt2')) {
variables_binning$index = stringr::str_remove(variables_binning$index, pattern = '.[0-9]{1,2}.bt2|.rev.[0-9]{1,2}.bt2')
output$index_binning_out <-
shiny::renderText(variables_binning$index)
variables_binning$activate_start2 = T
} else{
output$index_binning_out <-
shiny::renderText(
paste(
'<b><p style="color:#FF0000";> selected file does not belong to a bowtie2 index.</b></p>'
)
)
variables$activate_start2 = F
}
} else{
variables$activate_start2 = F
output$index_binning_out <-
shiny::renderText(NULL)
}
})
###select out folder
shiny::observeEvent(input$out_binning,
{
if (!is.numeric(input$out_binning)) {
#recover out directory
variables_binning$out = shinyFiles::parseDirPath(selection = input$out_binning, roots = roots)
#render out dir
output$Output_binning_out <-
shiny::renderText(variables_binning$out)
variables_binning$activate_start3 = T
} else{
variables_binning$activate_start3 = F
output$Output_binning_out <-
shiny::renderText(NULL)
}
})
#select bamfile folder
shiny::observeEvent(input$Bam_binning, {
if (!is.numeric(input$Bam_binning)) {
#recover fastq directory
variables_binning$Bam_dir = shinyFiles::parseDirPath(selection = input$Bam_binning, roots = roots)
#check for fastq files
if (length(list.files(path = variables_binning$Bam_dir, pattern = '.bam')) >
0) {
output$Bam_binning_out <-
shiny::renderText(variables_binning$Bam_dir)
variables_binning$activate_start4 = T
} else{
output$Bam_binning_out <-
shiny::renderText(
paste(
'<b><p style="color:#FF0000";> selected directory does not contain fastq files</b></p>'
)
)
variables_binning$activate_start4 = F
}
} else{
variables_binning$activate_start4 = F
output$Bam_binning_out <-
shiny::renderText(NULL)
variables_binning$Bam_dir = NULL
}
})
#activate start4 if Manual parameters are selected
shiny::observeEvent(input$Param_binning, {
if (input$Param_binning == 'Auto') {
variables_binning$activate_start4 = F
} else{
variables_binning$activate_start4 = T
}
})
#select blacklist
shiny::observeEvent(input$Blacklist_binning, {
if (!is.numeric(input$Blacklist_binning)) {
#recover index directory
variables_binning$blacklist = shinyFiles::parseFilePaths(selection = input$Blacklist_binning,
roots = roots)
variables_binning$blacklist = variables_binning$blacklist$datapath
#check that the selected file is actually part of an index
if (Kronos.scRT::right_format(
file_path = variables_binning$blacklist,
columns_to_check = 3,
logical = T
)) {
output$Blacklist_binning_out <-
shiny::renderText(variables_binning$blacklist)
variables_binning$activate_start5 = T
} else{
output$Blacklist_binning_out <-
shiny::renderText(
paste(
'<b><p style="color:#FF0000";> selected file does not have the required format.</b></p>'
)
)
variables_binning$activate_start5 = F
}
} else{
output$Blacklist_binning_out <-
shiny::renderText(NULL)
variables_binning$activate_start5 = T
variables_binning$blacklist = NULL
}
})
##activate start
shiny::observeEvent(
c(
variables_binning$activate_start1,
variables_binning$activate_start2,
variables_binning$activate_start3,
variables_binning$activate_start4,
variables_binning$activate_start5
),
{
if (variables_binning$activate_start1 &
variables_binning$activate_start2 &
variables_binning$activate_start3 &
variables_binning$activate_start4 &
variables_binning$activate_start5)
{
shinyjs::enable('run_binning')
} else
{
shinyjs::disable('run_binning')
}
}
)
#manual parameters change
shiny::observeEvent(input$Reads_type_binning, {
variables_binning$read_type = input$Reads_type_binning
})
shiny::observeEvent(input$Read_size_binning, {
variables_binning$read_size = input$Read_size_binning
})
shiny::observeEvent(input$Fragment_size_binning, {
variables_binning$frag_size = input$Fragment_size_binning
})
#run
shiny::observeEvent(input$run_binning, {
if (input$run_binning > 0) {
#disable buttons
shinyjs::disable('RefGenome_binning')
shinyjs::disable('index_binning')
shinyjs::disable('out_binning')
shinyjs::disable('Param_binning')
shinyjs::disable('Bam_binning')
shinyjs::disable('Coverage_binning')
shinyjs::disable('Reads_type_binning')
shinyjs::disable('Read_size_binning')
shinyjs::disable('Fragment_size_binning')
shinyjs::disable('Cores_binning')
shinyjs::disable('Mappability_binning')
shinyjs::disable('ErrorRate_binning')
shinyjs::disable('Blacklist_binning')
shinyjs::disable('chr_prefix_binning')
shinyjs::disable('chr_range_binning')
shinyjs::disable('BinSize_binning')
shinyjs::disable('run_binning')
#start binning
bins = Kronos.scRT::binning(
RefGenome = variables_binning$fasta,
bowtie2_index = variables_binning$index,
bin_size = input$BinSize_binning * 1000,
read_size = variables_binning$read_size,
fragment_size = variables_binning$frag_size,
paired_ends = variables_binning$read_type == 'PE',
directory_to_bamfiles = variables_binning$Bam_dir,
tmp_dir = file.path(variables_binning$out, 'tmp'),
upper_mappability_th = max(input$Mappability_binning),
lower_mappability_th = min(input$Mappability_binning),
black_list = variables_binning$blacklist,
coverage = input$Coverage_binning,
errorRate = input$ErrorRate_binning / 100,
cores = input$Cores_binning,
chr_prefix = ifelse(
input$chr_prefix_binning == '',
NULL,
input$chr_prefix_binning
),
chr_range = input$chr_range_binning,
return_estimated_param = T
)
#if directory_to_bamfiles is given return parameters
param = bins$param
bins = bins$bins
#write file
readr::write_tsv(bins, file.path(
variables_binning$out,
paste0(
basename(variables_binning$index),
'_',
input$BinSize_binning,
'kb_bins_coverage_',
input$Coverage_binning,
'X_',
paste0(
'reads_',
param$read_size,
'bp_',
ifelse(
param$paired_ends,
paste0('PE_fragmentSize_', param$fragment_size, 'bp_')
,
'SE_'
)
),
ifelse(
!is.null(variables_binning$blacklist),
'blacklisted_',
''
),
paste0(
'error_rate_',
input$ErrorRate_binning,
'_min_mappability_',
min(input$Mappability_binning),
'_max_mappability_',
max(input$Mappability_binning)
),
'.tsv'
)
))
#enable
shinyjs::enable('RefGenome_binning')
shinyjs::enable('index_binning')
shinyjs::enable('out_binning')
shinyjs::enable('Param_binning')
shinyjs::enable('Bam_binning')
shinyjs::enable('Coverage_binning')
shinyjs::enable('Reads_type_binning')
shinyjs::enable('Read_size_binning')
shinyjs::enable('Fragment_size_binning')
shinyjs::enable('Cores_binning')
shinyjs::enable('Mappability_binning')
shinyjs::enable('ErrorRate_binning')
shinyjs::enable('Blacklist_binning')
shinyjs::enable('chr_prefix_binning')
shinyjs::enable('chr_range_binning')
shinyjs::enable('run_binning')
shinyjs::enable('BinSize_binning')
}
})
}
#### CN
{
#set shiny Files buttons
shinyFiles::shinyDirChoose(
input = input,
id = 'Bamdir_CN',
session = session,
roots = roots,
defaultRoot = 'Home'
)
shinyFiles::shinyDirChoose(
input = input,
id = 'Output_CN',
session = session,
roots = roots,
defaultRoot = 'Home'
)
shinyFiles::shinyFileChoose(
input = input,
id = 'Bins_CN',
session = session,
roots = roots,
defaultRoot = 'Home'
)
shinyFiles::shinyFileChoose(
input = input,
id = 'ChrSize_CN',
session = session,
roots = roots,
defaultRoot = 'Home'
)
#set variables
variables_cn = reactiveValues(
Bamdir_CN = NULL,
Output_CN = NULL,
Bins_CN = NULL,
ChrSize_CN = NULL,
Samples = dplyr::tibble(),
run_ok1 = F,
run_ok2 = F,
sample_counter = 0,
group_counter = 0
)
# ui if user wants fix ploidy average
output$FixAveragePloidy = shiny::renderUI({
shiny::req(input$Ploidy_Restrictions_CN == 'Fix Average Ploidy')
shiny::fluidRow(shiny::column(
width = 3,
shiny::numericInput(
inputId = 'meanPloidy_CN',
label = 'Average ploidy',
value = 2,
min = 1,
step = 0.1,
width = '100%'
)
))
})
# ui if user wants fix ploidy average
output$FixPloidyRange = shiny::renderUI({
shiny::req(input$Ploidy_Restrictions_CN == 'Fix Ploidy Range')
shiny::fluidRow(
shiny::column(
width = 3,
shiny::numericInput(
inputId = 'minPloidy_CN',
label = 'Min accepted ploidy',
value = 2,
min = 0,
step = 0.1,
width = '100%'
)
),
shiny::column(
width = 3,
shiny::numericInput(
inputId = 'maxPloidy_CN',
label = 'Max accepted ploidy',
value = 8,
min = 0,
step = 0.1,
width = '100%'
)
)
)
})
#set output folder
shiny::observeEvent(input$Output_CN, {
if (!is.numeric(input$Output_CN)) {
variables_cn$Output_CN = shinyFiles::parseDirPath(roots = roots, selection = input$Output_CN)
} else{
variables_cn$Output_CN = NULL
}
output$Output_CN = shiny::renderText(variables_cn$Output_CN)
})
#set BinsFile
shiny::observeEvent(input$Bins_CN, {
if (!is.numeric(input$Bins_CN)) {
variables_cn$Bins_CN = shinyFiles::parseFilePaths(roots = roots, selection = input$Bins_CN)
variables_cn$Bins_CN = variables_cn$Bins_CN$datapath
variables_cn$Bins_CN = Kronos.scRT::right_format(
file_path = variables_cn$Bins_CN,
columns_to_check = c(
'chr',
'start',
'end',
'mappability',
'mappability_th',
'gc_frequency',
'type'
),
wrong_message = paste(
'<b><p style="color:#FF0000";>',
variables_cn$Bins_CN,
'does not have the right format!</p></b>'
),
rigth_message = variables_cn$Bins_CN
)
} else{
variables_cn$Bins_CN = NULL
}
output$Bins_CN = shiny::renderText(variables_cn$Bins_CN)
})
#authorize run if binsfile is good
shiny::observeEvent(variables_cn$Bins_CN, {
if (!is.null(variables_cn$Bins_CN) &
stringr::str_detect(string = variables_cn$Bins_CN,
pattern = 'does not have the right format!</p></b>',
negate = T)) {
variables_cn$run_ok1 = T
} else{
variables_cn$run_ok1 = F
}
})
#set Chrsize
shiny::observeEvent(input$ChrSize_CN, {
if (!is.numeric(input$ChrSize_CN)) {
variables_cn$ChrSize_CN = shinyFiles::parseFilePaths(roots = roots, selection = input$ChrSize_CN)
variables_cn$ChrSize_CN = variables_cn$ChrSize_CN$datapath
variables_cn$ChrSize_CN = Kronos.scRT::right_format(
file_path = variables_cn$ChrSize_CN,
columns_to_check = c('chr',
'size'),
wrong_message = paste(
'<b><p style="color:#FF0000";>',
variables_cn$ChrSize_CN,
'does not have the right format!</p></b>'
),
rigth_message = variables_cn$ChrSize_CN
)
} else{
variables_cn$ChrSize_CN = NULL
}
output$ChrSize_CN = shiny::renderText(variables_cn$ChrSize_CN)
})
#authorize run if Chrsize is good
shiny::observeEvent(variables_cn$ChrSize_CN, {
if (!is.null(variables_cn$ChrSize_CN) &
stringr::str_detect(
string = variables_cn$ChrSize_CN,
pattern = 'does not have the right format!</p></b>',
negate = T
)) {
variables_cn$run_ok2 = T
} else{
variables_cn$run_ok2 = F
}
})
#set BAM folder
shiny::observeEvent(input$Bamdir_CN, {
if (!is.numeric(input$Bamdir_CN)) {
variables_cn$Bamdir_CN = shinyFiles::parseDirPath(roots = roots, selection = input$Bamdir_CN)
#check if file contains BAMS
if (!any(stringr::str_detect(
string = list.files(variables_cn$Bamdir_CN),
pattern = '.bam$'
))) {
variables_cn$Bamdir_CN = paste(
'<b><p style="color:#FF0000";>',
variables_cn$Bamdir_CN,
'does not contain bam files</p></b>'
)
shinyjs::disable('AddSample_CN')
} else{
shinyjs::enable('AddSample_CN')
}
} else{
variables_cn$Bamdir_CN = NULL
shinyjs::disable('AddSample_CN')
}
output$Bamdir_CN = shiny::renderText(variables_cn$Bamdir_CN)
})
#add samples
shiny::observeEvent(input$AddSample_CN, {
if (input$AddSample_CN > 0) {
shinyjs::disable('AddSample_CN')
variables_cn$Samples = rbind(
variables_cn$Samples,
dplyr::tibble(
Basename = input$basename_CN,
Group = input$group_CN,
Bamfiles = variables_cn$Bamdir_CN
)
)
output$Samples_CN = shiny::renderTable(variables_cn$Samples)
#reset interface
if (any(
stringr::str_detect(
string = variables_cn$Samples$Basename,
pattern = '^Exp_{0,1}[0-9]{0,3}$'
)
)) {
variables_cn$sample_counter = variables_cn$sample_counter + 1
shiny::updateTextInput(
inputId = 'basename_CN',
value = paste0('Exp_', variables_cn$sample_counter)
)
} else{
shinyjs::reset(input$basename_CN)
}
if (any(
stringr::str_detect(string = variables_cn$Samples$Group, pattern = '^Exp_{0,1}[0-9]{0,3}$')
)) {
variables_cn$group_counter = variables_cn$group_counter + 1
shiny::updateTextInput(
inputId = 'group_CN',
value = paste0('Exp_', variables_cn$group_counter)
)
} else{
shinyjs::reset(input$group_CN)
}
}
})
#activate run
shiny::observeEvent(
c(
variables_cn$Samples,
variables_cn$run_ok1,
variables_cn$run_ok2,
variables_cn$Output_CN
),
{
if (variables_cn$run_ok1 &
variables_cn$run_ok2 &
nrow(variables_cn$Samples) > 0 &
!is.null(variables_cn$Output_CN)) {
shinyjs::enable('Run_CN')
} else{
shinyjs::disable('Run_CN')
}
}
)
shiny::observeEvent(input$Run_CN, {
if (input$Run_CN > 0) {
#load df
Bins_CN = readr::read_tsv(variables_cn$Bins_CN)
ChrSize_CN = readr::read_tsv(variables_cn$ChrSize_CN)
shinyjs::disable('Run_CN')
for (i in 1:nrow(variables_cn$Samples)) {
if (input$Ploidy_Restrictions_CN != 'Fix Average Ploidy') {
results = Kronos.scRT::CallCNV(
directory = variables_cn$Samples$Bamfiles[i],
bins = Bins_CN,
chrom_size = ChrSize_CN,
basename = variables_cn$Samples$Basename[i],
group = variables_cn$Samples$Group[i],
tmp_dir = file.path(variables_cn$Output_CN, 'tmp'),
min_n_reads = input$min_reads_CN,
mim_mean_CN_accepted = ifelse(
is.null(input$minPloidy_CN),
2,
input$minPloidy_CN
),
max_mean_CN_accepted = ifelse(
is.null(input$maxPloidy_CN),
8,
input$maxPloidy_CN
),
chr_prefix = input$CHR_CN,
chr_range = input$CHR_RANGE_CN,
cores = input$Cores_CN
)
} else{
results = Kronos.scRT::CallCNV(
directory = variables_cn$Samples$Bamfiles[i],
bins = Bins_CN,
chrom_size = ChrSize_CN,
basename = variables_cn$Samples$Basename[i],
group = variables_cn$Samples$Group[i],
tmp_dir = file.path(variables_cn$Output_CN, 'tmp'),
min_n_reads = input$min_reads_CN,
ploidy = ifelse(
is.null(input$meanPloidy_CN),
2,
input$meanPloidy_CN
),
chr_prefix = input$CHR_CN,
chr_range = input$CHR_RANGE_CN,
cores = input$Cores_CN
)
}
dir = file.path(variables_cn$Output_CN,
variables_cn$Samples$Basename[i])
if (!dir.exists(dir)) {
dir.create(dir)
}
results$PerCell %>%
readr::write_csv(file = file.path(
dir,
paste0(variables_cn$Samples$Basename[i], '_PerCell.csv')
))
results$CNV %>%
readr::write_tsv(file = file.path(
dir,
paste0(variables_cn$Samples$Basename[i], '_scCNV.tsv')
))
}
}
})
}
}
# Run the application
shiny::shinyApp(ui = ui,
server = server)
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