Nothing
inst/shiny/ui.R
In MesKit: A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic alterations
#required packages
suppressMessages(library(shiny))
suppressMessages(library(DT))
suppressMessages(library(shinydashboard))
suppressMessages(library(shinyWidgets))
suppressMessages(library(shinycssloaders))
suppressMessages(library(shinyBS))
suppressMessages(library(MesKit))
suppressMessages(library(BSgenome.Hsapiens.UCSC.hg19))
#sider bar----
sidebar <- dashboardSidebar(
width = 300,
sidebarMenu(id="sidername",selected='home',
menuItem(strong("Home"), tabName = "home", icon = icon("home")),
menuItem(strong("Input data"), tabName = "input", icon = icon("gear")),
menuItem(strong("Mutational landscape"), tabName = "AL", icon = icon("bar-chart")),
menuItem(strong("ITH evaluation"), tabName = "ITH", icon = icon("bar-chart")),
menuItem(strong("Metastatic routes inference"), tabName = "clone", icon = icon("bar-chart")),
menuItem(strong("PhyloTree-based analysis"), tabName = "tree", icon = icon("tree"))
)
)
#shinydashboar
bodyHome <- tabItem("home",
fluidRow(
box(
width = 12,
status = "info",
solidHeader = TRUE,
title = div(strong("Introduction"),style = "font-size:2em; font-weight:500;"),
p("Cancer develops as a result of the accumulation of genetic aberrations, which promotes the generation of distinct subpopulations of tumor cells and shapes intra-tumor heterogeneity (ITH). ITH is involves in tumor growth, progression, invasion, and metastasis, presenting one of the most significant barriers to accurate diagnoses and effective treatments of cancers. Therefore, dissecting and interpreting ITH of tumor dynamics is one of the major tasks in cancer research. Here, we present MesKit, an R-based package, to provide commonly used analysis and visualization modules in MRS study.",
style = "font-size:18px; font-weight:500;line-height:40px;"),
br()
)
),
fluidRow(
box(
width = 12,
status = "info",
solidHeader = TRUE,
title = div(strong("Overview of MesKit"),style = "font-size:2em; font-weight:500;"),
fluidRow(
column(
width = 6,
div(img(src = "image/MesKit_workflow.png", width = "90%",height = "72%"),
style="text-align: center;float:left;margin:0;padding:0")
),
column(
width = 5,
div(
br(),
br(),
br(),
br(),
h3(strong("With this MesKit Shiny APP:")),
p("- Characterize mutational landscape",br(),
"- Quantify heterogeneity within or between tumors from the same patient",br(),
"- Infer metastatic routes",br(),
"- Perform mutational signature analysis on different levels",br(),
"- Construct and visualize phylogenetic trees",
style = "font-size:18px; font-weight:500;line-height:50px;"),
style = "text-align: left;float:left;padding-left:0px;margin:0px"
)
)
)
)
)
)
bodyIP <- tabItem("input",
fluidRow(
column(
width = 12,
column(
width = 3,
box(
div(shiny::icon("gear"), strong("Input Section"), inline =TRUE,style = "font-size:27px; font-weight:500;"),
br(),
width = NULL,
fileInput(inputId = 'mafFile',
label = div(style = "font-size:1.5em; font-weight:600;",'MAF file',
tags$button(
Id = "iecontrol01",
type = "button",
class = "bttn-material-circle",
class = "btn action-button",
list(tags$img(src = "image/button.png",width = "22px",height = "22px")),
style = " background-position: center;padding:0;margin-bottom:7px;"
)
),
placeholder = "Example: CRC_HZ.maf",
width = 400),
fileInput(inputId = 'clinFile',
label = div(style = "font-size:1.5em; font-weight:600;",'Clinical file',
tags$button(
Id = "iecontrol_clin",
type = "button",
class = "bttn-material-circle",
class = "btn action-button",
list(tags$img(src = "image/button.png",width = "22px",height = "22px")),
style = " background-position: center;padding:0;margin-bottom:7px;"
)
),
placeholder = "Example: CRC_HZ.clin.txt",
width = 400),
checkboxInput('useccffile', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px",
'CCF file',
tags$button(
Id = "iecontrol02",
type = "button",
class = "bttn-material-circle",
class = "btn action-button",
list(tags$img(src = "image/button.png",width = "22px",height = "22px")),
style = " background-position: center;padding:0;margin-bottom:7px;"
)),
value = FALSE,width = 400),
bsTooltip(id = "useccffile",
title = "CCF file of somatic mutations. Default NULL.",
placement = "top",
trigger = "hover"),
conditionalPanel(
condition = "input.useccffile == true",
fileInput('ccfFile',label = '',placeholder = "Example: CRC_HZ.ccf.tsv", width = 400),
checkboxInput('ccfFile_use_indel_ccf',label = div(style = "font-size:1.5em; font-weight:600;padding-left:15px ", 'Use indel ccf'),value = FALSE),
bsTooltip(id = "ccfFile_use_indel_ccf",
title = "Whether use indel in ccfFile. Default FALSE.",
placement = "top",
trigger = "hover"),
),
selectInput('ref', label = div(style = "font-size:1.5em; font-weight:600; ", 'Genome reference'),
choices = c('hg18','hg19','hg38'),selected = "hg19", width = 400),
bsTooltip(id = "ref",
title = "Human reference genome versions of hg18,hg19 or hg38 by UCSC",
placement = "top",
trigger = "hover"),
actionBttn('submit1',div(
strong("Upload data"),align = 'center'))
)
),
column(
width = 9,
box(
width = NULL,
uiOutput("datapreview"),
# DT::dataTableOutput('maftable', width = '100%')
uiOutput("ie1"),
uiOutput("ie2"),
uiOutput("ie_clin"),
)
)
)
)
)
bodyITH <- tabItem("ITH",
fluidRow(
column(
width = 3,
box(
width = NULL,
conditionalPanel(
condition = "input.tith == 'ith_mathscore'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
uiOutput("mathscore_patientid_ui"),
checkboxInput('mathscore_withintumor',
value = FALSE,
label = div(style = "font-size:1.5em; font-weight:600; padding-left:12px", 'Within tumor'),
width = 500),
bsTooltip(id = "mathscore_withintumor",
title = "Calculate MATH score within tumors in each patients",
placement = "top",
trigger = "hover"),
checkboxInput('mathscore_useadjvaf',
label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use adjusted vaf'),
value = FALSE,
width = 400),
bsTooltip(id = "mathscore_useadjvaf",
title = "Use adjusted VAF in analysis when adjusted VAF or CCF is available. Default FALSE.",
placement = "top",
trigger = "hover"),
checkboxInput('mathscore_usetumorsamplelabel', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use tumor sample label'),value = FALSE, width = 400),
bsTooltip(id = "mathscore_usetumorsamplelabel",
title = "Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Label'.",
placement = "top",
trigger = "hover"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min vaf")),
tags$td(width = "60%", textInput(inputId = "mathscore_minvaf", value = 0, label = NULL)))
),
bsTooltip(id = "mathscore_minvaf",
title = "The minimum VAF for filtering variants. Default: 0. ",
placement = "top",
trigger = "hover"),
br(),
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit_mathscore", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
),
conditionalPanel(
condition = "input.tith == 'ith_vafcluster'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
uiOutput("vafcluster_patientid_ui"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min vaf")),
tags$td(width = "60%", textInput(inputId = "vafcluster_minvaf", value = 0, label = NULL)))
),
bsTooltip(id = "vafcluster_minvaf",
title = "The minimum value of VAF. Default: 0. Option: on the scale of 0 to 1.",
placement = "top",
trigger = "hover"),
# br(),
# tags$table(
# tags$tr(id = "inline",
# width = "100%",
# tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Max vaf")),
# tags$td(width = "60%", textInput(inputId = "vafcluster_maxvaf", value = 1, label = NULL)))
# ),
# bsTooltip(id = "vafcluster_maxvaf",
# title = "The maximum value of VAF. Default: 0. Option: on the scale of 0 to 1.",
# placement = "top",
# trigger = "hover"),
br(),
checkboxInput('vafcluster_withintumor',label = div(style = "font-size:1.5em; font-weight:600;padding-left:15px ", 'Within tumor'),value = FALSE),
bsTooltip(id = "vafcluster_withintumor",
title = "Cluster VAF within tumors in each patients,default is FALSE.",
placement = "top",
trigger = "hover"),
checkboxInput('vafcluster_useadjvaf', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use adjusted vaf'),value = FALSE, width = 400),
bsTooltip(id = "vafcluster_useadjvaf",
title = "Use adjusted VAF in analysis when adjusted VAF or CCF is available. Default FALSE.",
placement = "top",
trigger = "hover"),
checkboxInput('vafcluster_useccf', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use ccf'),value = FALSE, width = 400),
bsTooltip(id = "vafcluster_useccf",
title = "Cluster CCF. Default FALSE.",
placement = "top",
trigger = "hover"),
checkboxInput('vafcluster_usetumorsamplelabel', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use tumor sample label'),value = FALSE, width = 400),
bsTooltip(id = "vafcluster_usetumorsamplelabel",
title = "Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Label'.",
placement = "top",
trigger = "hover"),
fileInput(inputId = 'vafcluster_segfile',
label = div(style = "font-size:1.5em; font-weight:600; ", 'Segment file'),
width = 400),
sliderInput(inputId='vafcluster_width',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image width'),min = 400,max = 1000, value = 470, width = 500),
sliderInput(inputId='vafcluster_height',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image height'),min = 400,max = 1000, value = 470, width = 500),
br(),
br(),
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit3", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
),
conditionalPanel(
condition = "input.tith == 'ith_ccfauc'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
uiOutput("ccfauc_patientid_ui"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min ccf")),
tags$td(width = "60%", textInput(inputId = "ccfauc_minccf", value = 0, label = NULL)))
),
bsTooltip(id = "ccfauc_minccf",
title = "The minimum value of CCF. Default: 0.",
placement = "top",
trigger = "hover"),
br(),
checkboxInput('ccfauc_withintumor',
value = FALSE,
label = div(style = "font-size:1.5em; font-weight:600; padding-left:12px", 'Within tumor'),
width = 500),
bsTooltip(id = "ccfauc_withintumor",
title = "Calculate AUC within tumors in each patients, default is FALSE.",
placement = "top",
trigger = "hover"),
# checkboxInput('ccfauc_useadjvaf', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use adjusted vaf'),value = FALSE, width = 400),
# bsTooltip(id = "ccfauc_useadjvaf",
# title = "Use adjusted VAF in analysis when adjusted VAF or CCF is available. Default FALSE.",
# placement = "top",
# trigger = "hover"),
checkboxInput('ccfauc_usetumorsamplelabel', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use tumor sample label'),value = FALSE, width = 400),
bsTooltip(id = "ccfauc_usetumorsamplelabel",
title = "Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Label'.",
placement = "top",
trigger = "hover"),
sliderInput(inputId='ccfauc_width',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image width'),min = 400,max = 1000, value = 747, width = 500),
sliderInput(inputId='ccfauc_height',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image height'),min = 400,max = 1000, value = 560, width = 500),
br(),
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit_ccfauc", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
),
conditionalPanel(
condition = "input.tith == 'ith_calfst'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
uiOutput("calfst_patientid_ui"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min vaf")),
tags$td(width = "60%", textInput(inputId = "calfst_minvaf", value = 0, label = NULL)))
),
bsTooltip(id = "calfst_minvaf",
title = "Specify the minimum VAF_adj, default is 0.02.",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "Min total depth")),
tags$td(width = "40%", textInput(inputId = "calfst_mintotaldepth", value = 2, label = NULL)))
),
bsTooltip(id = "calfst_mintotaldepth",
title = "The minimum total allele depth for filtering variants. Default: 2.",
placement = "top",
trigger = "hover"),
checkboxInput('calfst_withinTumor',
value = FALSE,
label = div(style = "font-size:1.5em; font-weight:600; padding-left:12px", 'Within Tumor'),
width = 500),
bsTooltip(id = "calfst_withinTumor",
title = "Calculate fst within types in each patients,default is FALSE.",
placement = "top",
trigger = "hover"),
checkboxInput('calfst_useadjvaf', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use adjusted vaf'),value = FALSE, width = 400),
bsTooltip(id = "calfst_useadjvaf",
title = "Use adjusted VAF in analysis when adjusted VAF or CCF is available. Default FALSE.",
placement = "top",
trigger = "hover"),
checkboxInput('calfst_usecircle',
value = TRUE,
label = div(style = "font-size:1.5em; font-weight:600; padding-left:12px", 'Use circle'),
width = 500),
checkboxInput('calfst_usetumorsamplelabel', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use tumor sample label'),value = FALSE, width = 400),
bsTooltip(id = "calfst_usetumorsamplelabel",
title = "Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Label'.",
placement = "top",
trigger = "hover"),
bsTooltip(id = "calfst_usecircle",
title = "Logical (Default:TRUE). Whether to use circle as visualization method of correlation matrix",
placement = "top",
trigger = "hover"),
# tags$table(
# tags$tr(id = "inline",
# width = "100%",
# tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Title: ")),
# tags$td(width = "70%", textInput(inputId = "calfst_title", value = NULL, label = NULL)))
# ),
# bsTooltip(id = "calfst_title",
# title = "The title of the plot.",
# placement = "top",
# trigger = "hover"),
# br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "number.cex")),
tags$td(width = "50%", textInput(inputId = "calfst_numbercex", value = 8, label = NULL)))
),
bsTooltip(id = "calfst_numbercex",
title = "The size of text shown in correlation plot. Default 8.",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "number.col")),
tags$td(width = "50%", textInput(inputId = "calfst_numbercol", value = "#C77960", label = NULL)))
),
bsTooltip(id = "calfst_numbercol",
title = "The color of text shown in correlation plot. Default #C77960.",
placement = "top",
trigger = "hover"),
br(),
sliderInput(inputId='calfst_width',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image width'),min = 400,max = 1000, value = 560, width = 500),
sliderInput(inputId='calfst_height',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image height'),min = 400,max = 1000, value = 560, width = 500),
br(),
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit_calfst", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
),
conditionalPanel(
condition = "input.tith == 'ith_mutheatmap'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
uiOutput("mutheatmap_patientid_ui"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min vaf")),
tags$td(width = "60%", textInput(inputId = "mutheatmap_minvaf", value = 0, label = NULL)))
),
bsTooltip(id = "mutheatmap_minvaf",
title = "The minimum value of VAF. Default: 0. Option: on the scale of 0 to 1.",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min ccf")),
tags$td(width = "60%", textInput(inputId = "mutheatmap_minccf", value = 0, label = NULL)))
),
bsTooltip(id = "mutheatmap_minccf",
title = "The minimum value of CCF. Default: 0. Option: on the scale of 0 to 1.",
placement = "top",
trigger = "hover"),
br(),
checkboxInput('mutheatmap_useadjvaf', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use adjusted vaf'),value = FALSE, width = 400),
bsTooltip(id = "mutheatmap_useadjvaf",
title = "Use adjusted VAF in analysis when adjusted VAF or CCF is available. Default FALSE.",
placement = "top",
trigger = "hover"),
checkboxInput('mutheatmap_useccf',
value = FALSE,
label = div(style = "font-size:1.5em; font-weight:600; padding-left:12px", 'Use ccf'),
width = 500),
bsTooltip(id = "mutheatmap_useccf",
title = "Logical. If FALSE (default), print a binary heatmap of mutations. Otherwise, print a cancer cell frequency (CCF) heatmap.",
placement = "top",
trigger = "hover"),
checkboxInput('mutheatmap_usetumorsamplelabel', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use tumor sample label'),value = FALSE, width = 400),
bsTooltip(id = "mutheatmap_usetumorsamplelabel",
title = "Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Label'.",
placement = "top",
trigger = "hover"),
checkboxInput('mutheatmap_classByTumor', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Class by tumor'),value = FALSE,width = 400),
bsTooltip(id = "mutheatmap_classByTumor",
title = "FALSE(Default). Define shared pattern of mutations based on tumor types (TRUE) or samples (FALSE)",
placement = "top",
trigger = "hover"),
# bsTooltip(id = "mutheatmap_useccf",
# title = "Logical. If FALSE (default), print a binary heatmap of mutations. Otherwise, print a cancer cell frequency (CCF) heatmap.",
# placement = "top",
# trigger = "hover"),
# fileInput(inputId = 'mutheatmap_genelist',
# label = div(style = "font-size:1.5em; font-weight:600; ", 'Gene list file'),
# placeholder = "Default: IntOGen-DriverGenes_HC.tsv",
# width = 400),
uiOutput("mutheatmap_parameters_ui"),
# checkboxInput('mutheatmap_plotgenelist',
# value = FALSE,
# label = div(style = "font-size:1.5em; font-weight:600; padding-left:12px", 'Plot gene list'),
# width = 500),
# bsTooltip(id = "mutheatmap_plotgenelist",
# title = "If TRUE, plot heatmap with genes on geneList when geneList is not NULL.Default FALSE.",
# placement = "top",
# trigger = "hover"),
#
# checkboxInput('mutheatmap_showgene',
# value = FALSE,
# label = div(style = "font-size:1.5em; font-weight:600; padding-left:12px", 'Show gene'),
# width = 500),
# bsTooltip(id = "mutheatmap_showgene",
# title = "Show the name of genes next to the heatmap.Default FALSE.",
# placement = "top",
# trigger = "hover"),
#
# checkboxInput('mutheatmap_showgenelist',
# value = TRUE,
# label = div(style = "font-size:1.5em; font-weight:600; padding-left:12px", 'Show gene list'),
# width = 500),
# bsTooltip(id = "mutheatmap_showgenelist",
# title = "Show the names of gene on the geneList.Default TRUE.",
# placement = "top",
# trigger = "hover"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "60%", div(style = "font-size:1.5em; font-weight:600; ", "Mutation threshold")),
tags$td(width = "30%", textInput(inputId = "mutheatmap_mutthreshold", value = 150, label = NULL)))
),
bsTooltip(id = "mutheatmap_mutthreshold",
title = "show.gene and show.geneList will be FALSE when patient have more mutations than threshold.Default is 150.",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "Sample text size")),
tags$td(width = "40%", textInput(inputId = "mutheatmap_sampletextsize", value = 9, label = NULL)))
),
bsTooltip(id = "mutheatmap_sampletextsize",
title = "Size of sample name.Default 9.",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "Legend title size")),
tags$td(width = "40%", textInput(inputId = "mutheatmap_legendtitlesize", value = 10, label = NULL)))
),
bsTooltip(id = "mutheatmap_legendtitlesize",
title = "Size of legend title.Default 9.",
placement = "top",
trigger = "hover"),
br(),
sliderInput(inputId='mutheatmap_width',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image width'),min = 400,max = 1000, value = 700, width = 500),
sliderInput(inputId='mutheatmap_height',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image height'),min = 400,max = 1000, value = 560, width = 500),
br(),
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit_mutheatmap", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
),
conditionalPanel(
condition = "input.tith == 'caInput_calneidist'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
uiOutput("calneidist_patientid_ui"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min CCF")),
tags$td(width = "60%", textInput(inputId = "calneidist_minccf", value = 0, label = NULL)))
),
br(),
bsTooltip(id = "calneidist_minccf",
title = "Specify the minimum CCF, default is 0.08.",
placement = "top",
trigger = "hover"),
checkboxInput('calneidist_withintumor',
value = FALSE,
label = div(style = "font-size:1.5em; font-weight:600; padding-left:12px", 'Within Tumor'),
width = 500),
bsTooltip(id = "calneidist_withintumor",
title = "Calculate fst within tumors in each patients,default is FALSE.",
placement = "top",
trigger = "hover"),
checkboxInput('calneidist_useadjvaf', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use adjusted vaf'),value = FALSE, width = 400),
bsTooltip(id = "calneidist_useadjvaf",
title = "Use adjusted VAF in analysis when adjusted VAF or CCF is available. Default FALSE.",
placement = "top",
trigger = "hover"),
checkboxInput('calneidist_usecircle',
value = TRUE,
label = div(style = "font-size:1.5em; font-weight:600; padding-left:12px", 'Use circle'),
width = 500),
bsTooltip(id = "calneidist_usecircle",
title = "Logical (Default:TRUE). Whether to use circle as visualization method of correlation matrix",
placement = "top",
trigger = "hover"),
checkboxInput('calneidist_usetumorsamplelabel', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use tumor sample label'),value = FALSE, width = 400),
bsTooltip(id = "calneidist_usetumorsamplelabel",
title = "Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Label'.",
placement = "top",
trigger = "hover"),
# tags$table(
# tags$tr(id = "inline",
# width = "100%",
# tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Title: ")),
# tags$td(width = "70%", textInput(inputId = "calneidist_title", value = NULL, label = NULL)))
# ),
# bsTooltip(id = "calneidist_title",
# title = "The title of the plot.",
# placement = "top",
# trigger = "hover"),
# br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "number.cex")),
tags$td(width = "50%", textInput(inputId = "calneidist_numbercex", value = 8, label = NULL)))
),
bsTooltip(id = "calneidist_numbercex",
title = "The size of text shown in correlation plot. Default 8.",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "number.col")),
tags$td(width = "50%", textInput(inputId = "calneidist_numbercol", value = "#C77960", label = NULL)))
),
bsTooltip(id = "calneidist_numbercol",
title = "The color of text shown in correlation plot. Default #C77960.",
placement = "top",
trigger = "hover"),
br(),
sliderInput(inputId='calneidist_width',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image width'),min = 400,max = 1000, value = 560, width = 500),
sliderInput(inputId='calneidist_height',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image height'),min = 400,max = 1000, value = 560, width = 500),
br(),
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit_calneidist", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
)
)
),
column(
width = 9,
box(
width = NULL,
div(strong("ITH evaluation"),style = "font-size:27px; font-weight:500;"),
p("Understanding the origin and development of intra-tumor heterogeneity is clinically important, which has the potential to yield insights to guide therapeutic strategies. MesKit has integrated several metrics to estimate ITH within region or between regions borrowed from published research and population genetics.",
style = "font-size:20px; font-weight:500;line-height:40px;"),
tabBox(
id = 'tith',
height = "100%",
width = "100%",
selected = "ith_mathscore",
side = "left",
tabPanel(
title = div(icon("chart-bar"), "MATH score", style = "font-size:1.5em; font-weight:600; "),
value = "ith_mathscore",
uiOutput("mathscore.patientlist"),
DT::dataTableOutput('mathScore'),
br(),
br(),
uiOutput("msdb")
),
tabPanel(
title = div(icon("image"), "Mut clustering", style = "font-size:1.5em; font-weight:600; "),
value = "ith_vafcluster",
uiOutput("vafcluster.patientlist"),
uiOutput("vafcluster_table_ui"),
uiOutput("vafcluster.samplelist"),
div(plotOutput("vaf",height = "100%", width = "100%"),align = "left"),
br(),
uiOutput("vcdb")
),
tabPanel(
title = div(icon("image"), "AUC of CCF", style = "font-size:1.5em; font-weight:600; "),
value = "ith_ccfauc",
uiOutput('ccfauc.patientlist'),
uiOutput("ccfauc_table_ui"),
div(plotOutput("ccfauc_plot",height = "100%", width = "100%"),align = "left") ,
uiOutput("ccfauc_db_ui")
),
tabPanel(
title = div(icon("image"), "Fixation index", style = "font-size:1.5em; font-weight:600; "),
value = "ith_calfst",
uiOutput('calfst.patientlist'),
uiOutput("calfst_pair_table_ui"),
div(plotOutput("calfst_plot",height = "100%", width = "100%"),align = "left") ,
uiOutput("calfst_db_ui")
# uiOutput("calfst_avg_table_ui"),
),
tabPanel(
title = div(icon("image"), "Nei's distance", style = "font-size:1.5em; font-weight:600; "),
value = "caInput_calneidist",
uiOutput('calneidist.patientlist'),
uiOutput("calneidist_pair_table_ui"),
div(plotOutput("calneidist_plot",height = "100%", width = "100%"),align = "left") ,
uiOutput("calneidist_db_ui")
# uiOutput("calneidist_avg_table_ui"),
),
tabPanel(
title = div(icon("image"), "Heatmap", style = "font-size:1.5em; font-weight:600; "),
value = "ith_mutheatmap",
uiOutput('mutheatmap.patientlist'),
div(plotOutput("mutheatmap_plot",height = "100%", width = "100%"),align = "left") ,
uiOutput("mutheatmap_db_ui")
)
)
)
)
)
)
bodyAL <- tabItem("AL",
fluidRow(
column(
width = 3,
box(
width = NULL,
conditionalPanel(
condition = "input.al_tabbox == 'pannel_plotmutprofile'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
uiOutput("plotmutprofile.patientlist"),
selectInput("plotmutprofile_class", label = div(style = "font-size:1.5em; font-weight:600; ", "Class"),
choices = c("SP","CS","SPCS"),
selected = "SP"),
bsTooltip(id = "plotmutprofile_class",
title = 'The class which would be represented, default is "SP" (Shared pattern: Public/Shared/Private),other options: "CS" (Clonal status: Clonal/Subclonl) and "SPCS".',
placement = "top",
trigger = "hover"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "Top genes count")),
tags$td(width = "40%", textInput(inputId = "plotmutprofile_topGenesCount", value = 10, label = NULL)))
),
bsTooltip(id = "plotmutprofile_topGenesCount",
title = "The number of genes print, default is 10",
placement = "top",
trigger = "hover"),
br(),
checkboxInput('plotmutprofile_usegenelist', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Gene list'),value = FALSE,width = 400),
bsTooltip(id = "plotmutprofile_usegenelist",
title = "A list of genes to restrict the analysis. Default NULL.",
placement = "top",
trigger = "hover"),
conditionalPanel(
condition = "input.plotmutprofile_usegenelist == true",
fileInput(inputId = 'plotmutprofile_genelist',
label = div(style = "font-size:1.5em; font-weight:600; ", 'Gene list file'),
placeholder = "Example: IntOGen-DriverGenes_COREAD.tsv",
width = 400)
),
checkboxInput('plotmutprofile_classByTumor', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Class by tumor'),value = FALSE,width = 400),
bsTooltip(id = "plotmutprofile_classByTumor",
title = "FALSE(Default). Define shared pattern of mutations based on tumor types (TRUE) or samples (FALSE)",
placement = "top",
trigger = "hover"),
checkboxInput('plotmutprofile_remove_empty_columns', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Remove empty columns'),value = TRUE,width = 400),
bsTooltip(id = "plotmutprofile_remove_empty_columns",
title = "Whether remove the samples without alterations",
placement = "top",
trigger = "hover"),
checkboxInput('plotmutprofile_remove_empty_rows', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Remove empty rows'),value = TRUE,width = 400),
bsTooltip(id = "plotmutprofile_remove_empty_rows",
title = "Whether remove the genes without alterations.",
placement = "top",
trigger = "hover"),
checkboxInput('plotmutprofile_showColnames', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Show column names'),value = TRUE,width = 400),
bsTooltip(id = "plotmutprofile_showColnames",
title = "TRUE(Default). Show sample names of columns.",
placement = "top",
trigger = "hover"),
checkboxInput('plotmutprofile_usetumorsamplelabel', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use tumor sample label'),value = FALSE, width = 400),
bsTooltip(id = "plotmutprofile_useadjvaf",
title = "Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Label'.",
placement = "top",
trigger = "hover"),
sliderInput('plotmutprofile_width', label = div(style = "font-size:1.5em; font-weight:600; ", 'Image width'), min = 400,max = 1200, value = 900,width = 500),
sliderInput('plotmutprofile_height', label = div(style = "font-size:1.5em; font-weight:600; ", 'Image height'), min = 400,max = 1200, value = 900,width = 500),
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit_plotmutprofile", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
),
conditionalPanel(
condition = "input.al_tabbox == 'pannel_plotcna'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
fileInput(inputId = 'plotcna_segfile',
label = div(style = "font-size:1.5em; font-weight:600;",'Segment file',
tags$button(
Id = "iecontrol_seg",
type = "button",
class = "bttn-material-circle",
class = "btn action-button",
list(tags$img(src = "image/button.png",width = "22px",height = "22px")),
style = " background-position: center;padding:0;margin-bottom:7px;"
)
),
placeholder = "Example: CRC_HZ.seg.txt",
width = 400),
# fileInput(inputId = 'plotcna_segfile',
# label = div(style = "font-size:1.5em; font-weight:600; ",
# 'Segment file'),
# width = 400),
checkboxInput('plotmutprofile_usegisticAmpGenes', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Gistic amplification genes'),value = FALSE,width = 400),
bsTooltip(id = "plotmutprofile_usegisticAmpGenes",
title = "Amplification Genes file generated by GISTIC.",
placement = "top",
trigger = "hover"),
conditionalPanel(
condition = "input.plotmutprofile_usegisticAmpGenes == true",
fileInput(inputId = 'plotcna_gisticAmpGenesFile',
label = '',
placeholder = "Example: LIHC_amp_genes.conf_99.txt",
width = 400)
),
checkboxInput('plotmutprofile_usegisticDelGenes', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Gistic deletion genes'),value = FALSE,width = 400),
bsTooltip(id = "plotmutprofile_usegisticDelGenes",
title = "Deletion Genes file generated by GISTIC.",
placement = "top",
trigger = "hover"),
conditionalPanel(
condition = "input.plotmutprofile_usegisticDelGenes == true",
fileInput(inputId = 'plotcna_gisticDelGenesFile',
label = '',
placeholder = "Example: LIHC_del_genes.conf_99.txt",
width = 400)
),
checkboxInput('plotmutprofile_usegisticAllLesions', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Gistic all lesions'),value = FALSE,width = 400),
bsTooltip(id = "plotmutprofile_usegisticAllLesions",
title = "Information of all lesions generated by GISTIC.",
placement = "top",
trigger = "hover"),
conditionalPanel(
condition = "input.plotmutprofile_usegisticAllLesions == true",
fileInput(inputId = 'plotcna_gisticAllLesionsFile',
label = '',
placeholder = "Example: LIHC_all_lesions.conf_99.txt",
width = 400)
),
selectInput('plotcna_refBuild', label = div(style = "font-size:1.5em; font-weight:600; ", 'Genome reference'),
choices = c('hg18','hg19','hg38'),selected = "hg19", width = 400),
bsTooltip(id = "plotcna_refBuild",
title = "Human reference genome versions of hg18, hg19 or hg38 by UCSC. Default: hg19.",
placement = "top",
trigger = "hover"),
uiOutput("plotcna_gistic_parameters_ui"),
br(),
uiOutput("plotcna.patientlist"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "Sample text size")),
tags$td(width = "40%", textInput(inputId = "plotcna_sampletextsize", value = 11, label = NULL)))
),
bsTooltip(id = "plotcna_sampletextsize",
title = "Size of sample name.Default 11.",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "Legend text size")),
tags$td(width = "40%", textInput(inputId = "plotcna_legendtextsize", value = 9, label = NULL)))
),
bsTooltip(id = "plotcna_legendtextsize",
title = "Size of legend text.Default 9.",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "Legend title size")),
tags$td(width = "40%", textInput(inputId = "plotcna_legendtitlesize", value = 11, label = NULL)))
),
bsTooltip(id = "plotcna_legendtitlesize",
title = "Size of legend title.Default 11.",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "Sample bar size")),
tags$td(width = "40%", textInput(inputId = "plotcna_samplebarheight", value = 0.5, label = NULL)))
),
bsTooltip(id = "plotcna_samplebarheight",
title = "Bar height of each sample.Default 0.5.",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "70%", div(style = "font-size:1.5em; font-weight:600; ", "Chromosome bar size")),
tags$td(width = "30%", textInput(inputId = "plotcna_chrombarheight", value = 0.5, label = NULL)))
),
bsTooltip(id = "plotcna_chrombarheight",
title = "Bar height of each chromosome.Default 0.5.",
placement = "top",
trigger = "hover"),
br(),
checkboxInput('plotcna_showrownames',label = div(style = "font-size:1.5em; font-weight:600;padding-left:15px ", 'Show row names'),value = TRUE),
checkboxInput('plotcna_usetumorsamplelabel', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use tumor sample label'),value = FALSE, width = 400),
bsTooltip(id = "plotcna_usetumorsamplelabel",
title = "Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Label'.",
placement = "top",
trigger = "hover"),
checkboxInput('plotcna_removeempytchr', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Remove empty chromosome'),value = FALSE, width = 400),
bsTooltip(id = "plotcna_removeempytchr",
title = "Remove empty chromosomes that do not exist in samples. Default TRUE. ",
placement = "top",
trigger = "hover"),
sliderInput('plotcna_width', label = div(style = "font-size:1.5em; font-weight:600; ", 'Image width'), min = 400,max = 1200, value = 800,width = 500),
sliderInput('plotcna_height', label = div(style = "font-size:1.5em; font-weight:600; ", 'Image height'), min = 400,max = 1200, value = 800,width = 500),
br(),
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit_plotcna", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
),
)
),
column(
width = 9,
box(
width = NULL,
div(strong("Mutational landscape"),style = "font-size:27px; font-weight:500;"),
p("",
style = "font-size:20px; font-weight:500;line-height:40px;"),
tabBox(
id = 'al_tabbox',
selected = 'pannel_plotmutprofile',
side = 'left',
height = "100%",
width = "100%",
tabPanel(
value = 'pannel_plotmutprofile',
title = div(icon("image"), "Mutational profile",style = "font-size:1.5em; font-weight:600; "),
div(plotOutput('plotmutprofile_plot', height = "100%", width = "100%"), align = "left"),
br(),
uiOutput("plotmutprofile_download_button_ui")
),
tabPanel(
value = 'pannel_plotcna',
title = div(icon("image"), "CNA profile", style = "font-size:1.5em; font-weight:600; "),
uiOutput("ie_seg"),
uiOutput("plotcna_table_ui"),
div(plotOutput('plotcna_plot', height = "100%", width = "100%"), align = "left"),
br(),
uiOutput("plotcna_download_button_ui")
)
)
)
)
)
)
bodyclone <- tabItem('clone',
fluidRow(
column(
width = 3,
box(
width = NULL,
conditionalPanel(
condition = "input.clt == 'clone_compareccf'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
uiOutput("compareccf_patientid_ui"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min ccf")),
tags$td(width = "60%", textInput(inputId = "compareccf_minccf", value = 0, label = NULL)))
),
br(),
bsTooltip(id = "compareccf_minccf",
title = "The minimum value of ccf",
placement = "top",
trigger = "hover"),
checkboxInput('compareccf_usetumorsamplelabel', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use tumor sample label'),value = FALSE, width = 400),
bsTooltip(id = "compareccf_usetumorsamplelabel",
title = "Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Label'.",
placement = "top",
trigger = "hover"),
uiOutput("compareccf_pairbytumor_ui"),
# checkboxInput('compareccf_pairbytumor',
# value = FALSE,
# label = div(style = "font-size:1.5em; font-weight:600; padding-left:12px", 'Pair by tumor'),
# width = 500),
# bsTooltip(id = "compareccf_pairbytumor",
# title = "Compare CCF by tumor",
# placement = "top",
# trigger = "hover"),
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit_compareccf", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
),
conditionalPanel(
condition = "input.clt == 'clone_caljsi'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
uiOutput("caljsi_patientid_ui"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min ccf")),
tags$td(width = "60%", textInput(inputId = "caljsi_minccf", value = 0, label = NULL)))
),
bsTooltip(id = "caljsi_minccf",
title = "The minimum value of ccf",
placement = "top",
trigger = "hover"),
checkboxInput('caljsi_usetumorsamplelabel', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use tumor sample label'),value = FALSE, width = 400),
bsTooltip(id = "caljsi_usetumorsamplelabel",
title = "Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Label'.",
placement = "top",
trigger = "hover"),
uiOutput("caljsi_pairbytumor_ui"),
# checkboxInput('caljsi_pairbytumor',
# value = FALSE,
# label = div(style = "font-size:1.5em; font-weight:600; padding-left:12px", 'Pair by tumor'),
# width = 500),
# bsTooltip(id = "caljsi_pairbytumor",
# title = "calculate JSI by tumor",
# placement = "top",
# trigger = "hover"),
checkboxInput('caljsi_usecircle',
value = TRUE,
label = div(style = "font-size:1.5em; font-weight:600; padding-left:12px", 'Use circle'),
width = 500),
bsTooltip(id = "caljsi_usecircle",
title = "Logical (Default:TRUE). Whether to use circle as visualization method of correlation matrix",
placement = "top",
trigger = "hover"),
# tags$table(
# tags$tr(id = "inline",
# width = "100%",
# tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Title: ")),
# tags$td(width = "70%", textInput(inputId = "caljsi_title", value = NULL, label = NULL)))
# ),
# bsTooltip(id = "caljsi_title",
# title = "The title of the plot.",
# placement = "top",
# trigger = "hover"),
# br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "number.cex")),
tags$td(width = "40%", textInput(inputId = "caljsi_numbercex", value = 8, label = NULL)))
),
bsTooltip(id = "caljsi_numbercex",
title = "The size of text shown in correlation plot. Default 8.",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "number.col")),
tags$td(width = "40%", textInput(inputId = "caljsi_numbercol", value = "#C77960", label = NULL)))
),
bsTooltip(id = "caljsi_numbercol",
title = "The color of text shown in correlation plot. Default #C77960.",
placement = "top",
trigger = "hover"),
br(),
sliderInput(inputId='caljsi_width',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image width'),min = 400,max = 1000, value = 560, width = 500),
sliderInput(inputId='caljsi_height',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image height'),min = 400,max = 1000, value = 560, width = 500),
br(),
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit_caljsi", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
),
conditionalPanel(
condition = "input.clt == 'clone_testneutral'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
uiOutput("testneutral_patientid_ui"),
checkboxInput('testneutral_withintumor',div(style = "font-size:1.5em; font-weight:600; padding-left:15px ", 'Within Tumor'),value = FALSE),
bsTooltip(id = "testneutral_withintumor",
title = 'Test neutral within tumros in each patients,default is FALSE.',
placement = "top",
trigger = "hover"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "Min total depth: ")),
tags$td(width = "50%", textInput(inputId = "testneutral_mintotaldepth", value = 2, label = NULL)))
),
bsTooltip(id = "testneutral_mintotaldepth",
title = "The minimun total depth of coverage. Defalut: 2",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min vaf: ")),
tags$td(width = "70%", textInput(inputId = "testneutral_minvaf", value = 0.1, label = NULL)))
),
bsTooltip(id = "testneutral_minvaf",
title = "The minimum value of vaf",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Max vaf: ")),
tags$td(width = "70%", textInput(inputId = "testneutral_maxvaf", value = 0.3, label = NULL)))
),
bsTooltip(id = "testneutral_maxvaf",
title = "The maximum value of vaf",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "R2 threshold: ")),
tags$td(width = "50%", textInput(inputId = "testneutral_R2threshold", value = 0.98, label = NULL)))
),
bsTooltip(id = "testneutral_R2threshold",
title = "The threshod of R2 to decide whether a tumor follows neutral evolution. Default: 0.98",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "Min mut count: ")),
tags$td(width = "50%", textInput(inputId = "testneutral_minmutcount", value = 20, label = NULL)))
),
bsTooltip(id = "testneutral_minmutcount",
title = "The minimun number of subclonal mutations used to fit model. Default: 20",
placement = "top",
trigger = "hover"),
br(),
sliderInput(inputId='testneutral_width',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image width'),min = 400,max = 1000, value = 560, width = 500),
sliderInput(inputId='testneutral_height',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image height'),min = 400,max = 1000, value = 560, width = 500),
br(),
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit_testneutral", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
)
)
),
column(
width = 9,
box(
width = NULL,
div(strong("Metastatic routes inference"),style = "font-size:27px; font-weight:500;"),
p("Since metastasis is the ultimate cause of death for most patients, it is particularly important to gain a systematic understanding of how tumor disseminates and the scale of ongoing parallel evolution in metastatic and primary site. Here, we provide two functions to help distinguish monoclonal from polyclonal seeding. ",
style = "font-size:20px; font-weight:500;line-height:40px;"),
tabBox(
id = 'clt',
selected = 'clone_compareccf',
side = 'left',
height = "100%",
width = "100%",
tabPanel(
value = 'clone_compareccf',
title = div(icon("chart-bar"), "CCF comparison", style = "font-size:1.5em; font-weight:600; "),
uiOutput('compareccf.patientlist'),
uiOutput('compareccf.samplelist'),
br(),
uiOutput("compareccf_table_ui")
),
tabPanel(
title = div(icon("image"), "Jaccard similarity index", style = "font-size:1.5em; font-weight:600; "),
value = "clone_caljsi",
uiOutput('caljsi.patientlist'),
uiOutput("caljsi_pair_table_ui"),
br(),
div(plotOutput("caljsi_plot",height = "100%", width = "100%"),align = "left") ,
uiOutput("caljsi_db_ui")
)
# tabPanel(
# title = div(icon("box"), "testNeutral"),
# value = "clone_testneutral",
# uiOutput('testneutral.patientlist'),
# uiOutput("testneutral_table_ui"),
# br(),
# uiOutput('testneutral.samplelist'),
# uiOutput('warningMessage_testneutral'),
# div(plotOutput("testneutral_plot",height = "100%", width = "100%"),align = "center") ,
# uiOutput("testneutral_db_ui")
# )
)
)
)
)
)
bodytree <- tabItem('tree',
fluidRow(
column(
width = 3,
box(
width = NULL,
# conditionalPanel(
# condition = "input.sgt == 'S_getphylotree'",
# div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
# br(),
# selectInput("getphylotree_method", label = div(style = "font-size:1.5em; font-weight:600; ", "Tree construct method"),
# choices = c("NJ","MP","ML","FASTME.ols","FASTME.bal"),
# selected = "NJ"),
# bsTooltip(id = "getphylotree_method",
# title = "Approach to construct phylogenetic trees",
# placement = "top",
# trigger = "hover"),
# tags$table(
# tags$tr(id = "inline",
# width = "100%",
# tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min vaf: ")),
# tags$td(width = "70%", textInput(inputId = "getphylotree_minvaf", value = 0.02, label = NULL)))
# ),
# bsTooltip(id = "getphylotree_minvaf",
# title = "The minimum value of vaf",
# placement = "top",
# trigger = "hover"),
# br(),
# tags$table(
# tags$tr(id = "inline",
# width = "100%",
# tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min ccf: ")),
# tags$td(width = "70%", textInput(inputId = "getphylotree_minccf", value = 0, label = NULL)))
# ),
# bsTooltip(id = "getphylotree_minccf",
# title = "The minimum value of ccf",
# placement = "top",
# trigger = "hover"),
# br(),
# tags$table(
# tags$tr(id = "inline",
# width = "100%",
# tags$td(width = "60%", div(style = "font-size:1.5em; font-weight:600; ", "Boostrap repetitions: ")),
# tags$td(width = "40%", textInput(inputId = "getphylotree_bootstraprepnum", value = 100, label = NULL)))
# ),
# bsTooltip(id = "getphylotree_bootstraprepnum",
# title = "Bootstrap iterations. Default 100.",
# placement = "top",
# trigger = "hover"),
# br(),
# actionBttn('submit_getphylotree',div(
# strong("Get phylotree"),align = 'center'))
# ),
conditionalPanel(
condition = "input.sgt == 'S_plotphylotree'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
uiOutput("plotphylotree_patientid_ui"),
selectInput("plotphylotree_getphylotree_method", label = div(style = "font-size:1.5em; font-weight:600; ", "Tree construct method"),
choices = c("NJ","MP","ML","FASTME.ols","FASTME.bal"),
selected = "NJ"),
bsTooltip(id = "plotphylotree_getphylotree_method",
title = "Approach to construct phylogenetic trees",
placement = "top",
trigger = "hover"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min vaf")),
tags$td(width = "60%", textInput(inputId = "plotphylotree_getphylotree_minvaf", value = 0, label = NULL)))
),
bsTooltip(id = "plotphylotree_getphylotree_minvaf",
title = "The minimum value of vaf",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min ccf")),
tags$td(width = "60%", textInput(inputId = "plotphylotree_getphylotree_minccf", value = 0, label = NULL)))
),
bsTooltip(id = "plotphylotree_getphylotree_minccf",
title = "The minimum value of ccf",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "Boostrap repetitions")),
tags$td(width = "30%", textInput(inputId = "plotphylotree_getphylotree_bootstraprepnum", value = 100, label = NULL)))
),
bsTooltip(id = "plotphylotree_getphylotree_bootstraprepnum",
title = "Bootstrap iterations. Default 100.",
placement = "top",
trigger = "hover"),
br(),
selectInput("plotphylotree_branchcol", label = div(style = "font-size:1.5em; font-weight:600; ", "Branch color"),
choices = c("mutType",
"mutSig",
"NULL"),
selected = "mutType"),
bsTooltip(id = "plotphylotree_branchcol",
title = "Specify the colors of branches (Default: mutType). Other options: 'mutSig' for coloring branches by branch mutation signature;",
placement = "top",
trigger = "hover"),
conditionalPanel(
condition = "input.plotphylotree_branchcol == 'mutSig'",
selectInput("plotphylotree_signatureref", label = div(style = "font-size:1.5em; font-weight:600; ", "Signautre reference"),
choices = c("cosmic_v2",
"nature2013",
"exome_cosmic_v3"),
selected = "cosmic_v2"),
bsTooltip(id = "plotphylotree_signatureref",
title = 'signature reference',
placement = "top",
trigger = "hover"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "60%", div(style = "font-size:1.5em; font-weight:600; ", "Minimal mutation number")),
tags$td(width = "20%", textInput(inputId = "plotphylotree_minmutcount", value = 15, label = NULL)))
),
bsTooltip(id = "plotphylotree_minmutcount",
title = 'The threshold for the variants in a branch. Default 15.',
placement = "top",
trigger = "hover"),
),
checkboxInput('plotphylotree_showbootstrap',div(style = "font-size:1.5em; font-weight:600; padding-left:15px ", 'Show bootstrap value'),value = TRUE),
bsTooltip(id = "plotphylotree_showbootstrap",
title = 'Whether to add bootstrap value on internal nodes.',
placement = "top",
trigger = "hover"),
checkboxInput('plotphylotree_usetumorsamplelabel', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use tumor sample label'),value = FALSE, width = 400),
bsTooltip(id = "plotphylotree_usetumorsamplelabel",
title = "Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Label'.",
placement = "top",
trigger = "hover"),
checkboxInput('plotphylotree_show_scale_bar', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Show scale bar'),value = FALSE, width = 400),
bsTooltip(id = "plotphylotree_show_scale_bar",
title = "Logical (Default: FALSE). Whether to show scale bar.This function adds a horizontal bar giving the scale of the branch lengths to a plot on the current graphical device.",
placement = "top",
trigger = "hover"),
conditionalPanel(
condition = "input.plotphylotree_show_scale_bar == true",
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Scale bar x")),
tags$td(width = "60%", textInput(inputId = "plotphylotree_scale_bar_x", value = NULL, label = NULL)))
),
bsTooltip(id = "plotphylotree_scale_bar_x",
title = "The x location of scale bar.",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Scale bar y")),
tags$td(width = "60%", textInput(inputId = "plotphylotree_scale_bar_y", value = NULL, label = NULL)))
),
bsTooltip(id = "plotphylotree_scale_bar_y",
title = "The y location of scale bar.",
placement = "top",
trigger = "hover"),
br(),
),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min ratio")),
tags$td(width = "60%", textInput(inputId = "plotphylotree_minratio", value = 0.05, label = NULL)))
),
bsTooltip(id = "plotphylotree_minratio",
title = "Double (Default:1/20). If min.ratio is not NULL,all edge length of a phylogenetic tree should be greater than min.ratio*the longest edge length.If not, the edge length will be reset as min.ratio*longest edge length.",
placement = "top",
trigger = "hover"),
br(),
sliderInput(inputId='plotphylotree_width',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image width'),min = 300,max = 1200, value = 500, width = 500),
sliderInput(inputId='plotphylotree_height',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image height'),min = 300,max = 1200, value = 500, width = 500),
#
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit_plotphylotree", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
),
conditionalPanel(
condition = "input.sgt == 'S_comparetree'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
uiOutput("comparetree.patientlist"),
selectInput("comparetree_getphylotree_method1",
label = div(style = "font-size:1.5em; font-weight:600; ",
"Tree1 construct method"),
choices = c("NJ","MP","ML","FASTME.ols","FASTME.bal"),
selected = "NJ"),
bsTooltip(id = "comparetree_getphylotree_method1",
title = "Approach to construct phylogenetic trees",
placement = "top",
trigger = "hover"),
selectInput("comparetree_getphylotree_method2",
label = div(style = "font-size:1.5em; font-weight:600; ",
"Tree2 construct method"),
choices = c("NJ","MP","ML","FASTME.ols","FASTME.bal"),
selected = "MP"),
bsTooltip(id = "comparetree_getphylotree_method2",
title = "Approach to construct phylogenetic trees",
placement = "top",
trigger = "hover"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min vaf")),
tags$td(width = "60%", textInput(inputId = "comparetree_getphylotree_minvaf", value = 0, label = NULL)))
),
bsTooltip(id = "comparetree_getphylotree_minvaf",
title = "The minimum value of vaf",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min ccf")),
tags$td(width = "60%", textInput(inputId = "comparetree_getphylotree_minccf", value = 0, label = NULL)))
),
bsTooltip(id = "comparetree_getphylotree_minccf",
title = "The minimum value of ccf",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%",
div(style = "font-size:1.5em; font-weight:600; ",
"Boostrap repetitions")),
tags$td(width = "30%",
textInput(inputId = "comparetree_getphylotree_bootstraprepnum",
value = 100, label = NULL)))
),
bsTooltip(id = "comparetree_getphylotree_bootstraprepnum",
title = "Bootstrap iterations. Default 100.",
placement = "top",
trigger = "hover"),
br(),
# div(strong("Parameter(phyloTree2)"),style = "font-size:1.6em; font-weight:600;"),
# selectInput("comparetree_getphylotree_method2", label = div(style = "font-size:1.5em; font-weight:600; ", "Tree construct method"),
# choices = c("NJ","MP","ML","FASTME.ols","FASTME.bal"),
# selected = "MP"),
# bsTooltip(id = "comparetree_getphylotree_method2",
# title = "Approach to construct phylogenetic trees",
# placement = "top",
# trigger = "hover"),
# tags$table(
# tags$tr(id = "inline",
# width = "100%",
# tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min vaf: ")),
# tags$td(width = "70%", textInput(inputId = "comparetree_getphylotree_minvaf2", value = 0.02, label = NULL)))
# ),
# bsTooltip(id = "comparetree_getphylotree_minvaf2",
# title = "The minimum value of vaf",
# placement = "top",
# trigger = "hover"),
# br(),
# tags$table(
# tags$tr(id = "inline",
# width = "100%",
# tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min ccf: ")),
# tags$td(width = "70%", textInput(inputId = "comparetree_getphylotree_minccf2", value = 0, label = NULL)))
# ),
# bsTooltip(id = "comparetree_getphylotree_minccf2",
# title = "The minimum value of ccf",
# placement = "top",
# trigger = "hover"),
# br(),
# tags$table(
# tags$tr(id = "inline",
# width = "100%",
# tags$td(width = "60%", div(style = "font-size:1.5em; font-weight:600; ", "Boostrap repetitions: ")),
# tags$td(width = "40%", textInput(inputId = "comparetree_getphylotree_bootstraprepnum2", value = 100, label = NULL)))
# ),
# bsTooltip(id = "comparetree_getphylotree_bootstraprepnum2",
# title = "Bootstrap iterations. Default 100.",
# placement = "top",
# trigger = "hover"),
# br(),
# div(strong("Parameter(compareTree)"),style = "font-size:1.6em; font-weight:600;"),
checkboxInput('comparetree_showbootstrap',
div(style = "font-size:1.5em; font-weight:600; padding-left:15px ",
'Show bootstrap value'),value = FALSE),
bsTooltip(id = "comparetree_showbootstrap",
title = 'Whether to add bootstrap value on internal nodes.',
placement = "top",
trigger = "hover"),
checkboxInput('comparetree_usetumorsamplelabel', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use tumor sample label'),value = FALSE, width = 400),
bsTooltip(id = "comparetree_usetumorsamplelabel",
title = "Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Label'.",
placement = "top",
trigger = "hover"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min ratio")),
tags$td(width = "60%", textInput(inputId = "comparetree_minratio", value = 0.05, label = NULL)))
),
bsTooltip(id = "comparetree_minratio",
title = "Double (Default:1/20). If min.ratio is not NULL,all edge length of a phylogenetic tree should be greater than min.ratio*the longest edge length.If not, the edge length will be reset as min.ratio*longest edge length.",
placement = "top",
trigger = "hover"),
br(),
# textInput(inputId = "comparetree_commoncol",
# label = div(style = "font-size:1.5em; font-weight:600; ", 'Common color'),
# value = "red"),
# bsTooltip(id = "comparetree_commoncol",
# title = "Color of common branches.",
# placement = "right",
# trigger = "hover"),
sliderInput(inputId='comparetree_width',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image width'),min = 700,max = 1400, value = 1100, width = 500),
sliderInput(inputId='comparetree_height',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image height'),min = 400,max = 1000, value = 700, width = 500),
#
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit_comparetree", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
),
conditionalPanel(
condition = "input.sgt == 'S_treemutsig'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
uiOutput("treemutsig_patientid_ui"),
selectInput("treemutsig_getphylotree_method", label = div(style = "font-size:1.5em; font-weight:600; ", "Tree construct method"),
choices = c("NJ","MP","ML","FASTME.ols","FASTME.bal"),
selected = "NJ"),
bsTooltip(id = "treemutsig_getphylotree_method",
title = "Approach to construct phylogenetic trees",
placement = "top",
trigger = "hover"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min vaf")),
tags$td(width = "60%", textInput(inputId = "treemutsig_getphylotree_minvaf", value = 0, label = NULL)))
),
bsTooltip(id = "treemutsig_getphylotree_minvaf",
title = "The minimum value of vaf",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min ccf")),
tags$td(width = "60%", textInput(inputId = "treemutsig_getphylotree_minccf", value = 0, label = NULL)))
),
bsTooltip(id = "treemutsig_getphylotree_minccf",
title = "The minimum value of ccf",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "Boostrap repetitions")),
tags$td(width = "30%", textInput(inputId = "treemutsig_getphylotree_bootstraprepnum", value = 100, label = NULL)))
),
bsTooltip(id = "treemutsig_getphylotree_bootstraprepnum",
title = "Bootstrap iterations. Default 100.",
placement = "top",
trigger = "hover"),
br(),
selectInput('treemutsig_level', label = div(style = "font-size:1.5em; font-weight:600; ", 'Level'),
choices = c('1','2','3', '4', '5', '6'),selected = "2", width = 400),
bsTooltip(id = "treemutsig_level",
title = " Calculate mutation in different levels.'1': patient,'2':tumor,'3':sample,'4':branch,'5':mutation type.Default level '2'.",
placement = "top",
trigger = "hover"),
# checkboxInput('treemutsig_withintumor',label = div(style = "font-size:1.5em; font-weight:600;padding-left:15px ", 'Within tumor'),value = FALSE),
# bsTooltip(id = "treemutsig_withintumor",
# title = 'Exploring signatures within tumor. Default: FALSE.',
# placement = "top",
# trigger = "hover"),
selectInput("treemutsig_signatureref", label = div(style = "font-size:1.5em; font-weight:600; ", "Signautre reference"),
choices = c("cosmic_v2",
"nature2013",
"exome_cosmic_v3"),
selected = "cosmic"),
bsTooltip(id = "treemutsig_signatureref",
title = 'signature reference',
placement = "top",
trigger = "hover"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "85%", div(style = "font-size:1.5em; font-weight:600; ", "Minimal mutation number")),
tags$td(width = "15%", textInput(inputId = "treemutsig_minmutcount", value = 15, label = NULL)))
),
bsTooltip(id = "treemutsig_minmutcount",
title = 'The threshold for the variants in a branch. Default 15.',
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "Signature cutoff")),
tags$td(width = "30%", textInput(inputId = "treemutsig_signaturecutoff", value = 0.1, label = NULL)))
),
bsTooltip(id = "treemutsig_signaturecutoff",
title = 'Discard any signature contributions with a weight less than this amount.Default: 0.1.',
placement = "top",
trigger = "hover"),
br(),
selectInput("treemutsig_mode", label = div(style = "font-size:1.5em; font-weight:600; ", "Mode"),
choices = c('NULL',
'Original',
'Reconstructed',
'Difference'),
selected = "NULL"),
bsTooltip(id = "treemutsig_mode",
title = "type of mutation spectrum.Default: NULL. Options:'Original','Reconstructed' or 'Difference'",
placement = "top",
trigger = "hover"),
checkboxInput('treemutsig_usetumorsamplelabel', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use tumor sample label'),value = FALSE, width = 400),
bsTooltip(id = "treemutsig_usetumorsamplelabel",
title = "Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Label'.",
placement = "top",
trigger = "hover"),
sliderInput(inputId='treemutsig_width',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image width'),min = 400,max = 1000, value = 800, width = 500),
sliderInput(inputId='treemutsig_height',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image height'),min = 400,max = 1000, value = 560, width = 500),
br(),
br(),
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit_treemutsig", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
),
conditionalPanel(
condition = "input.sgt == 'S_muttrunkbranch'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
uiOutput("muttrunkbranch_patientid_ui"),
selectInput("muttrunkbranch_getphylotree_method", label = div(style = "font-size:1.5em; font-weight:600; ", "Tree construct method"),
choices = c("NJ","MP","ML","FASTME.ols","FASTME.bal"),
selected = "NJ"),
bsTooltip(id = "muttrunkbranch_getphylotree_method",
title = "Approach to construct phylogenetic trees",
placement = "top",
trigger = "hover"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min vaf")),
tags$td(width = "60%", textInput(inputId = "muttrunkbranch_getphylotree_minvaf", value = 0, label = NULL)))
),
bsTooltip(id = "muttrunkbranch_getphylotree_minvaf",
title = "The minimum value of vaf",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min ccf")),
tags$td(width = "60%", textInput(inputId = "muttrunkbranch_getphylotree_minccf", value = 0, label = NULL)))
),
bsTooltip(id = "muttrunkbranch_getphylotree_minccf",
title = "The minimum value of ccf",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "Boostrap repetitions")),
tags$td(width = "30%", textInput(inputId = "muttrunkbranch_getphylotree_bootstraprepnum", value = 100, label = NULL)))
),
bsTooltip(id = "muttrunkbranch_getphylotree_bootstraprepnum",
title = "Bootstrap iterations. Default 100.",
placement = "top",
trigger = "hover"),
checkboxInput('muttrunkbranch_ct',div(style = "font-size:1.5em; font-weight:600; padding-left:15px ", 'CT'),value = FALSE),
bsTooltip(id = "muttrunkbranch_ct",
title = 'Distinction between C>T at CpG and C>T at other sites, Default FALSE',
placement = "top",
trigger = "hover"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "P-value")),
tags$td(width = "60%", textInput(inputId = "muttrunkbranch_pvalue", value = 0.05, label = NULL)))
),
br(),
bsTooltip(id = "muttrunkbranch_pvalue",
title = "Confidence level of the interval for Fisher test. Default: 0.05.",
placement = "right",
trigger = "hover"),
sliderInput(inputId='muttrunkbranch_width',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image width'),min = 400,max = 1000, value = 470, width = 500),
sliderInput(inputId='muttrunkbranch_height',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image height'),min = 400,max = 1000, value = 470, width = 500),
br(),
br(),
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit_muttrunkbranch", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
)
)
),
column(
width = 9,
box(
width = NULL,
div(strong("PhyloTree-based analysis"),style = "font-size:27px; font-weight:500;"),
p("Systematic understanding of evolutionary relationship among regions plays a fundamental role in MRS study, where phylogenetic tree is the primary tool for describing these associations and interpreting ITH. MesKit is capable of constructing and comparing phylogenetic trees based on different methods, visualizing the rooted phylogenetic trees with annotation, as well as charactering mutational patterns based on phylogenetic trees.",
style = "font-size:20px; font-weight:500;line-height:40px;"),
tabBox(
id = 'sgt',
side = 'left',
selected = 'S_plotphylotree',
width = "100%",
height = "100%",
tabPanel(
title = div(icon("tree"), "Plot phylotree", style = "font-size:1.5em; font-weight:600; "),
value = 'S_plotphylotree',
uiOutput("phylotree.patientlist"),
div(plotOutput("phylotree_plot",height = "100%",width = "100%"),align = "left"),
br(),
uiOutput("phylotree_downloadbutton_ui")
),
tabPanel(
title = div(icon("tree"), "Compare tree", style = "font-size:1.5em; font-weight:600; "),
value = 'S_comparetree',
verbatimTextOutput("comparetree_dist"),
br(),
div(plotOutput('comparetree_plot', height = "100%", width = "100%"),align = "left"),
uiOutput('comparetree_db_ui')
# br(),
# uiOutput('treemutsig_table_ui')
),
tabPanel(
title = div(icon("image"), "Mutational signature", style = "font-size:1.5em; font-weight:600; "),
value = 'S_treemutsig',
# uiOutput('warningMessage_treemutsig'),
uiOutput("treemutsig.patientlist"),
uiOutput("treemutsig.samplelist"),
div(plotOutput('treemutsig_plot', height = "100%", width = "100%"),align = "left"),
uiOutput("treemutsig_download_button_ui"),
# br(),
# uiOutput('treemutsig_table_ui')
),
tabPanel(
title = div(icon("image"), "MutTrunkBranch", style = "font-size:1.5em; font-weight:600; "),
value = 'S_muttrunkbranch',
uiOutput("muttrunkbranch.patientlist"),
br(),
uiOutput('muttrunkbranch_table_ui'),
div(plotOutput('muttrunkbranch_plot', height = "100%", width = "100%"),align = "left"),
uiOutput("muttrunkbranch_download_button_ui")
)
)
)
)
)
)
#Main function----
dbHeader <- dashboardHeader(title = "MesKit", titleWidth = 300,
# tags$li(class = "dropdown", actionLink(inputId = "help", label = div(style = "font-size:15px; font-weight:400; ", "Help"))),
# tags$li(class = "dropdown", actionLink(inputId = "contact", label = div(style = "font-size:15px; font-weight:400; ", "Contact"))),
dropdownMenu(
type = "notifications",
icon = icon("question-circle"),
badgeStatus = NULL,
headerText = "Help:",
notificationItem("MesKit github page", icon = icon("file"),
href = "https://github.com/Niinleslie/MesKit")
),
dropdownMenu(
type = "notifications",
icon = icon("envelope"),
badgeStatus = NULL,
headerText = "",
tags$li(p("Mengni Liu, liumn5@mail2.sysu.edu.cn")),
tags$li(p("Jianyu Chen, chenjy327@mail2.sysu.edu.cn")),
tags$li(p("Xin Wang, wangx555@mail2.sysu.edu.cn")),
tags$li(p("Chengwei Wang, wangchw8@outlook.com"))
# notificationItem("Mengni Liu, liumn5@mail2.sysu.edu.cn, Sun Yat-sen university", icon = icon("user"),href = "liumn5@mail2.sysu.edu.cn"),
# notificationItem("Chengwei Wang, wangchw8@outlook.com, Sun Yat-sen university", icon = icon("user"),href = "wangchw8@outlook.com"),
# notificationItem("Jianyu Chen, chenjy327@mail2.sysu.edu.cn, Sun Yat-sen university", icon = icon("user"),href = "chenjy327@mail2.sysu.edu.cn"),
# notificationItem("Xin Wang, wangx555@mail2.sysu.edu.cn, Sun Yat-sen university", icon = icon("user"),href = "wangx555@mail2.sysu.edu.cn")
)
)
dbHeader$children[[2]]$children <- tags$a(href='https://github.com/Niinleslie/MesKit',
tags$img(src='image/logo.jpg',height='65',width='250'))
shinyUI(
dashboardPage(
skin = "blue",
header=dbHeader ,
sidebar=sidebar,
body=dashboardBody(
## add text behind the sidebar (design error)
tags$head(tags$style(HTML(
"/* logo */
.skin-blue .main-header .logo {
background-color: #3c8dbc;
}
/* logo when hovered */
.skin-blue .main-header .logo:hover {
background-color: #3c8dbc;
}
.textnvbar {
font-size: 20px;
line-height: 50px;
text-align: left;
font-family: 'Helvetica Neue',Helvetica,Arial,sans-serif;
padding: 0 15px;
overflow: hidden;
color: white;
}
.checkbox { /* checkbox is a div class*/
line-height: 25px;}
input[type='checkbox']{
width: 23px; /*Desired width*/
height: 23px; /*Desired height*/
line-height: 25px;
}
span {
line-height: 30px;
}
"))),
## change the style of the progress bar.
# tags$head(tags$style(
# type="text/css",
# ".progress.shiny-file-input-progress {
# height:5px;
# }
#
# .progress-bar {
# background-image: linear-gradient(to right, #77C7FF, #3c8dbc ) !important;
# background-size: auto !important;
# font-size:0px;
# height:5px;
# }"
# )),
tags$script(HTML('
$(document).ready(function() {
$("header").find("nav").append(\'<span class="textnvbar"> MesKit: A Tool Kit for Dissecting Cancer Evolution of Multi-region Tumor Biopsies through Somatic Alterations</span>\');
})
')),
tags$head(
tags$style(type="text/css", "#inline label{ display: table-cell; text-align: centers; vertical-align: middle; width=400; }
#inline .form-group { display: table-row; width=400; }"),
tags$style(HTML("
.shiny-output-error-validation {
color: brown;
}
.shiny-notification {
height: 200px;
width: 600px;
position:fixed;
font-size: 30px;
top: calc(50% - 100px);
left: calc(50% + 100px);
}
.dt-right {
text-align: justify !important;
}
.shiny-output-error-validation {
color: green;
font-size:27px;
font-weight:500;
}
.main-sidebar { font-size: 20px; }
table.dataTable tbody th, table.dataTable tbody td {
padding: 10px 1.5em !important;
}
.tooltip {
min-width: 15em !important;
}
.progress-message, .progress-detail {
display: block !important;
}
# .shiny-notification-close {
# float: right;/*image size adjust */
# font-weight: bold;
# font-size: 30px;
# bottom: 9px;
# position: relative;
# padding-left: 4px;
# color: #444;
# cursor: default;
# }
# .pipediv{
# width:900px;
# height:500px;
# }
# .pipediv .pipe{
# float:left;
# }
# .pipediv .pipe img{
# width:500px;
# height:500px;
# }
# .pipetext{
#
# }
")),
tags$link(rel = "stylesheet", type = "text/css", href = "main.css")
),
tabItems(
bodyHome,
bodyIP,
bodyAL,
bodyITH,
bodyclone,
# bodyfunction,
bodytree
# bodySurvival
)
)
)
)
Try the MesKit package in your browser
Any scripts or data that you put into this service are public.
MesKit documentation built on March 28, 2021, 6 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
#required packages
suppressMessages(library(shiny))
suppressMessages(library(DT))
suppressMessages(library(shinydashboard))
suppressMessages(library(shinyWidgets))
suppressMessages(library(shinycssloaders))
suppressMessages(library(shinyBS))
suppressMessages(library(MesKit))
suppressMessages(library(BSgenome.Hsapiens.UCSC.hg19))
#sider bar----
sidebar <- dashboardSidebar(
width = 300,
sidebarMenu(id="sidername",selected='home',
menuItem(strong("Home"), tabName = "home", icon = icon("home")),
menuItem(strong("Input data"), tabName = "input", icon = icon("gear")),
menuItem(strong("Mutational landscape"), tabName = "AL", icon = icon("bar-chart")),
menuItem(strong("ITH evaluation"), tabName = "ITH", icon = icon("bar-chart")),
menuItem(strong("Metastatic routes inference"), tabName = "clone", icon = icon("bar-chart")),
menuItem(strong("PhyloTree-based analysis"), tabName = "tree", icon = icon("tree"))
)
)
#shinydashboar
bodyHome <- tabItem("home",
fluidRow(
box(
width = 12,
status = "info",
solidHeader = TRUE,
title = div(strong("Introduction"),style = "font-size:2em; font-weight:500;"),
p("Cancer develops as a result of the accumulation of genetic aberrations, which promotes the generation of distinct subpopulations of tumor cells and shapes intra-tumor heterogeneity (ITH). ITH is involves in tumor growth, progression, invasion, and metastasis, presenting one of the most significant barriers to accurate diagnoses and effective treatments of cancers. Therefore, dissecting and interpreting ITH of tumor dynamics is one of the major tasks in cancer research. Here, we present MesKit, an R-based package, to provide commonly used analysis and visualization modules in MRS study.",
style = "font-size:18px; font-weight:500;line-height:40px;"),
br()
)
),
fluidRow(
box(
width = 12,
status = "info",
solidHeader = TRUE,
title = div(strong("Overview of MesKit"),style = "font-size:2em; font-weight:500;"),
fluidRow(
column(
width = 6,
div(img(src = "image/MesKit_workflow.png", width = "90%",height = "72%"),
style="text-align: center;float:left;margin:0;padding:0")
),
column(
width = 5,
div(
br(),
br(),
br(),
br(),
h3(strong("With this MesKit Shiny APP:")),
p("- Characterize mutational landscape",br(),
"- Quantify heterogeneity within or between tumors from the same patient",br(),
"- Infer metastatic routes",br(),
"- Perform mutational signature analysis on different levels",br(),
"- Construct and visualize phylogenetic trees",
style = "font-size:18px; font-weight:500;line-height:50px;"),
style = "text-align: left;float:left;padding-left:0px;margin:0px"
)
)
)
)
)
)
bodyIP <- tabItem("input",
fluidRow(
column(
width = 12,
column(
width = 3,
box(
div(shiny::icon("gear"), strong("Input Section"), inline =TRUE,style = "font-size:27px; font-weight:500;"),
br(),
width = NULL,
fileInput(inputId = 'mafFile',
label = div(style = "font-size:1.5em; font-weight:600;",'MAF file',
tags$button(
Id = "iecontrol01",
type = "button",
class = "bttn-material-circle",
class = "btn action-button",
list(tags$img(src = "image/button.png",width = "22px",height = "22px")),
style = " background-position: center;padding:0;margin-bottom:7px;"
)
),
placeholder = "Example: CRC_HZ.maf",
width = 400),
fileInput(inputId = 'clinFile',
label = div(style = "font-size:1.5em; font-weight:600;",'Clinical file',
tags$button(
Id = "iecontrol_clin",
type = "button",
class = "bttn-material-circle",
class = "btn action-button",
list(tags$img(src = "image/button.png",width = "22px",height = "22px")),
style = " background-position: center;padding:0;margin-bottom:7px;"
)
),
placeholder = "Example: CRC_HZ.clin.txt",
width = 400),
checkboxInput('useccffile', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px",
'CCF file',
tags$button(
Id = "iecontrol02",
type = "button",
class = "bttn-material-circle",
class = "btn action-button",
list(tags$img(src = "image/button.png",width = "22px",height = "22px")),
style = " background-position: center;padding:0;margin-bottom:7px;"
)),
value = FALSE,width = 400),
bsTooltip(id = "useccffile",
title = "CCF file of somatic mutations. Default NULL.",
placement = "top",
trigger = "hover"),
conditionalPanel(
condition = "input.useccffile == true",
fileInput('ccfFile',label = '',placeholder = "Example: CRC_HZ.ccf.tsv", width = 400),
checkboxInput('ccfFile_use_indel_ccf',label = div(style = "font-size:1.5em; font-weight:600;padding-left:15px ", 'Use indel ccf'),value = FALSE),
bsTooltip(id = "ccfFile_use_indel_ccf",
title = "Whether use indel in ccfFile. Default FALSE.",
placement = "top",
trigger = "hover"),
),
selectInput('ref', label = div(style = "font-size:1.5em; font-weight:600; ", 'Genome reference'),
choices = c('hg18','hg19','hg38'),selected = "hg19", width = 400),
bsTooltip(id = "ref",
title = "Human reference genome versions of hg18,hg19 or hg38 by UCSC",
placement = "top",
trigger = "hover"),
actionBttn('submit1',div(
strong("Upload data"),align = 'center'))
)
),
column(
width = 9,
box(
width = NULL,
uiOutput("datapreview"),
# DT::dataTableOutput('maftable', width = '100%')
uiOutput("ie1"),
uiOutput("ie2"),
uiOutput("ie_clin"),
)
)
)
)
)
bodyITH <- tabItem("ITH",
fluidRow(
column(
width = 3,
box(
width = NULL,
conditionalPanel(
condition = "input.tith == 'ith_mathscore'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
uiOutput("mathscore_patientid_ui"),
checkboxInput('mathscore_withintumor',
value = FALSE,
label = div(style = "font-size:1.5em; font-weight:600; padding-left:12px", 'Within tumor'),
width = 500),
bsTooltip(id = "mathscore_withintumor",
title = "Calculate MATH score within tumors in each patients",
placement = "top",
trigger = "hover"),
checkboxInput('mathscore_useadjvaf',
label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use adjusted vaf'),
value = FALSE,
width = 400),
bsTooltip(id = "mathscore_useadjvaf",
title = "Use adjusted VAF in analysis when adjusted VAF or CCF is available. Default FALSE.",
placement = "top",
trigger = "hover"),
checkboxInput('mathscore_usetumorsamplelabel', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use tumor sample label'),value = FALSE, width = 400),
bsTooltip(id = "mathscore_usetumorsamplelabel",
title = "Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Label'.",
placement = "top",
trigger = "hover"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min vaf")),
tags$td(width = "60%", textInput(inputId = "mathscore_minvaf", value = 0, label = NULL)))
),
bsTooltip(id = "mathscore_minvaf",
title = "The minimum VAF for filtering variants. Default: 0. ",
placement = "top",
trigger = "hover"),
br(),
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit_mathscore", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
),
conditionalPanel(
condition = "input.tith == 'ith_vafcluster'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
uiOutput("vafcluster_patientid_ui"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min vaf")),
tags$td(width = "60%", textInput(inputId = "vafcluster_minvaf", value = 0, label = NULL)))
),
bsTooltip(id = "vafcluster_minvaf",
title = "The minimum value of VAF. Default: 0. Option: on the scale of 0 to 1.",
placement = "top",
trigger = "hover"),
# br(),
# tags$table(
# tags$tr(id = "inline",
# width = "100%",
# tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Max vaf")),
# tags$td(width = "60%", textInput(inputId = "vafcluster_maxvaf", value = 1, label = NULL)))
# ),
# bsTooltip(id = "vafcluster_maxvaf",
# title = "The maximum value of VAF. Default: 0. Option: on the scale of 0 to 1.",
# placement = "top",
# trigger = "hover"),
br(),
checkboxInput('vafcluster_withintumor',label = div(style = "font-size:1.5em; font-weight:600;padding-left:15px ", 'Within tumor'),value = FALSE),
bsTooltip(id = "vafcluster_withintumor",
title = "Cluster VAF within tumors in each patients,default is FALSE.",
placement = "top",
trigger = "hover"),
checkboxInput('vafcluster_useadjvaf', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use adjusted vaf'),value = FALSE, width = 400),
bsTooltip(id = "vafcluster_useadjvaf",
title = "Use adjusted VAF in analysis when adjusted VAF or CCF is available. Default FALSE.",
placement = "top",
trigger = "hover"),
checkboxInput('vafcluster_useccf', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use ccf'),value = FALSE, width = 400),
bsTooltip(id = "vafcluster_useccf",
title = "Cluster CCF. Default FALSE.",
placement = "top",
trigger = "hover"),
checkboxInput('vafcluster_usetumorsamplelabel', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use tumor sample label'),value = FALSE, width = 400),
bsTooltip(id = "vafcluster_usetumorsamplelabel",
title = "Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Label'.",
placement = "top",
trigger = "hover"),
fileInput(inputId = 'vafcluster_segfile',
label = div(style = "font-size:1.5em; font-weight:600; ", 'Segment file'),
width = 400),
sliderInput(inputId='vafcluster_width',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image width'),min = 400,max = 1000, value = 470, width = 500),
sliderInput(inputId='vafcluster_height',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image height'),min = 400,max = 1000, value = 470, width = 500),
br(),
br(),
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit3", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
),
conditionalPanel(
condition = "input.tith == 'ith_ccfauc'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
uiOutput("ccfauc_patientid_ui"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min ccf")),
tags$td(width = "60%", textInput(inputId = "ccfauc_minccf", value = 0, label = NULL)))
),
bsTooltip(id = "ccfauc_minccf",
title = "The minimum value of CCF. Default: 0.",
placement = "top",
trigger = "hover"),
br(),
checkboxInput('ccfauc_withintumor',
value = FALSE,
label = div(style = "font-size:1.5em; font-weight:600; padding-left:12px", 'Within tumor'),
width = 500),
bsTooltip(id = "ccfauc_withintumor",
title = "Calculate AUC within tumors in each patients, default is FALSE.",
placement = "top",
trigger = "hover"),
# checkboxInput('ccfauc_useadjvaf', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use adjusted vaf'),value = FALSE, width = 400),
# bsTooltip(id = "ccfauc_useadjvaf",
# title = "Use adjusted VAF in analysis when adjusted VAF or CCF is available. Default FALSE.",
# placement = "top",
# trigger = "hover"),
checkboxInput('ccfauc_usetumorsamplelabel', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use tumor sample label'),value = FALSE, width = 400),
bsTooltip(id = "ccfauc_usetumorsamplelabel",
title = "Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Label'.",
placement = "top",
trigger = "hover"),
sliderInput(inputId='ccfauc_width',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image width'),min = 400,max = 1000, value = 747, width = 500),
sliderInput(inputId='ccfauc_height',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image height'),min = 400,max = 1000, value = 560, width = 500),
br(),
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit_ccfauc", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
),
conditionalPanel(
condition = "input.tith == 'ith_calfst'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
uiOutput("calfst_patientid_ui"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min vaf")),
tags$td(width = "60%", textInput(inputId = "calfst_minvaf", value = 0, label = NULL)))
),
bsTooltip(id = "calfst_minvaf",
title = "Specify the minimum VAF_adj, default is 0.02.",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "Min total depth")),
tags$td(width = "40%", textInput(inputId = "calfst_mintotaldepth", value = 2, label = NULL)))
),
bsTooltip(id = "calfst_mintotaldepth",
title = "The minimum total allele depth for filtering variants. Default: 2.",
placement = "top",
trigger = "hover"),
checkboxInput('calfst_withinTumor',
value = FALSE,
label = div(style = "font-size:1.5em; font-weight:600; padding-left:12px", 'Within Tumor'),
width = 500),
bsTooltip(id = "calfst_withinTumor",
title = "Calculate fst within types in each patients,default is FALSE.",
placement = "top",
trigger = "hover"),
checkboxInput('calfst_useadjvaf', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use adjusted vaf'),value = FALSE, width = 400),
bsTooltip(id = "calfst_useadjvaf",
title = "Use adjusted VAF in analysis when adjusted VAF or CCF is available. Default FALSE.",
placement = "top",
trigger = "hover"),
checkboxInput('calfst_usecircle',
value = TRUE,
label = div(style = "font-size:1.5em; font-weight:600; padding-left:12px", 'Use circle'),
width = 500),
checkboxInput('calfst_usetumorsamplelabel', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use tumor sample label'),value = FALSE, width = 400),
bsTooltip(id = "calfst_usetumorsamplelabel",
title = "Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Label'.",
placement = "top",
trigger = "hover"),
bsTooltip(id = "calfst_usecircle",
title = "Logical (Default:TRUE). Whether to use circle as visualization method of correlation matrix",
placement = "top",
trigger = "hover"),
# tags$table(
# tags$tr(id = "inline",
# width = "100%",
# tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Title: ")),
# tags$td(width = "70%", textInput(inputId = "calfst_title", value = NULL, label = NULL)))
# ),
# bsTooltip(id = "calfst_title",
# title = "The title of the plot.",
# placement = "top",
# trigger = "hover"),
# br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "number.cex")),
tags$td(width = "50%", textInput(inputId = "calfst_numbercex", value = 8, label = NULL)))
),
bsTooltip(id = "calfst_numbercex",
title = "The size of text shown in correlation plot. Default 8.",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "number.col")),
tags$td(width = "50%", textInput(inputId = "calfst_numbercol", value = "#C77960", label = NULL)))
),
bsTooltip(id = "calfst_numbercol",
title = "The color of text shown in correlation plot. Default #C77960.",
placement = "top",
trigger = "hover"),
br(),
sliderInput(inputId='calfst_width',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image width'),min = 400,max = 1000, value = 560, width = 500),
sliderInput(inputId='calfst_height',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image height'),min = 400,max = 1000, value = 560, width = 500),
br(),
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit_calfst", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
),
conditionalPanel(
condition = "input.tith == 'ith_mutheatmap'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
uiOutput("mutheatmap_patientid_ui"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min vaf")),
tags$td(width = "60%", textInput(inputId = "mutheatmap_minvaf", value = 0, label = NULL)))
),
bsTooltip(id = "mutheatmap_minvaf",
title = "The minimum value of VAF. Default: 0. Option: on the scale of 0 to 1.",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min ccf")),
tags$td(width = "60%", textInput(inputId = "mutheatmap_minccf", value = 0, label = NULL)))
),
bsTooltip(id = "mutheatmap_minccf",
title = "The minimum value of CCF. Default: 0. Option: on the scale of 0 to 1.",
placement = "top",
trigger = "hover"),
br(),
checkboxInput('mutheatmap_useadjvaf', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use adjusted vaf'),value = FALSE, width = 400),
bsTooltip(id = "mutheatmap_useadjvaf",
title = "Use adjusted VAF in analysis when adjusted VAF or CCF is available. Default FALSE.",
placement = "top",
trigger = "hover"),
checkboxInput('mutheatmap_useccf',
value = FALSE,
label = div(style = "font-size:1.5em; font-weight:600; padding-left:12px", 'Use ccf'),
width = 500),
bsTooltip(id = "mutheatmap_useccf",
title = "Logical. If FALSE (default), print a binary heatmap of mutations. Otherwise, print a cancer cell frequency (CCF) heatmap.",
placement = "top",
trigger = "hover"),
checkboxInput('mutheatmap_usetumorsamplelabel', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use tumor sample label'),value = FALSE, width = 400),
bsTooltip(id = "mutheatmap_usetumorsamplelabel",
title = "Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Label'.",
placement = "top",
trigger = "hover"),
checkboxInput('mutheatmap_classByTumor', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Class by tumor'),value = FALSE,width = 400),
bsTooltip(id = "mutheatmap_classByTumor",
title = "FALSE(Default). Define shared pattern of mutations based on tumor types (TRUE) or samples (FALSE)",
placement = "top",
trigger = "hover"),
# bsTooltip(id = "mutheatmap_useccf",
# title = "Logical. If FALSE (default), print a binary heatmap of mutations. Otherwise, print a cancer cell frequency (CCF) heatmap.",
# placement = "top",
# trigger = "hover"),
# fileInput(inputId = 'mutheatmap_genelist',
# label = div(style = "font-size:1.5em; font-weight:600; ", 'Gene list file'),
# placeholder = "Default: IntOGen-DriverGenes_HC.tsv",
# width = 400),
uiOutput("mutheatmap_parameters_ui"),
# checkboxInput('mutheatmap_plotgenelist',
# value = FALSE,
# label = div(style = "font-size:1.5em; font-weight:600; padding-left:12px", 'Plot gene list'),
# width = 500),
# bsTooltip(id = "mutheatmap_plotgenelist",
# title = "If TRUE, plot heatmap with genes on geneList when geneList is not NULL.Default FALSE.",
# placement = "top",
# trigger = "hover"),
#
# checkboxInput('mutheatmap_showgene',
# value = FALSE,
# label = div(style = "font-size:1.5em; font-weight:600; padding-left:12px", 'Show gene'),
# width = 500),
# bsTooltip(id = "mutheatmap_showgene",
# title = "Show the name of genes next to the heatmap.Default FALSE.",
# placement = "top",
# trigger = "hover"),
#
# checkboxInput('mutheatmap_showgenelist',
# value = TRUE,
# label = div(style = "font-size:1.5em; font-weight:600; padding-left:12px", 'Show gene list'),
# width = 500),
# bsTooltip(id = "mutheatmap_showgenelist",
# title = "Show the names of gene on the geneList.Default TRUE.",
# placement = "top",
# trigger = "hover"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "60%", div(style = "font-size:1.5em; font-weight:600; ", "Mutation threshold")),
tags$td(width = "30%", textInput(inputId = "mutheatmap_mutthreshold", value = 150, label = NULL)))
),
bsTooltip(id = "mutheatmap_mutthreshold",
title = "show.gene and show.geneList will be FALSE when patient have more mutations than threshold.Default is 150.",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "Sample text size")),
tags$td(width = "40%", textInput(inputId = "mutheatmap_sampletextsize", value = 9, label = NULL)))
),
bsTooltip(id = "mutheatmap_sampletextsize",
title = "Size of sample name.Default 9.",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "Legend title size")),
tags$td(width = "40%", textInput(inputId = "mutheatmap_legendtitlesize", value = 10, label = NULL)))
),
bsTooltip(id = "mutheatmap_legendtitlesize",
title = "Size of legend title.Default 9.",
placement = "top",
trigger = "hover"),
br(),
sliderInput(inputId='mutheatmap_width',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image width'),min = 400,max = 1000, value = 700, width = 500),
sliderInput(inputId='mutheatmap_height',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image height'),min = 400,max = 1000, value = 560, width = 500),
br(),
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit_mutheatmap", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
),
conditionalPanel(
condition = "input.tith == 'caInput_calneidist'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
uiOutput("calneidist_patientid_ui"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min CCF")),
tags$td(width = "60%", textInput(inputId = "calneidist_minccf", value = 0, label = NULL)))
),
br(),
bsTooltip(id = "calneidist_minccf",
title = "Specify the minimum CCF, default is 0.08.",
placement = "top",
trigger = "hover"),
checkboxInput('calneidist_withintumor',
value = FALSE,
label = div(style = "font-size:1.5em; font-weight:600; padding-left:12px", 'Within Tumor'),
width = 500),
bsTooltip(id = "calneidist_withintumor",
title = "Calculate fst within tumors in each patients,default is FALSE.",
placement = "top",
trigger = "hover"),
checkboxInput('calneidist_useadjvaf', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use adjusted vaf'),value = FALSE, width = 400),
bsTooltip(id = "calneidist_useadjvaf",
title = "Use adjusted VAF in analysis when adjusted VAF or CCF is available. Default FALSE.",
placement = "top",
trigger = "hover"),
checkboxInput('calneidist_usecircle',
value = TRUE,
label = div(style = "font-size:1.5em; font-weight:600; padding-left:12px", 'Use circle'),
width = 500),
bsTooltip(id = "calneidist_usecircle",
title = "Logical (Default:TRUE). Whether to use circle as visualization method of correlation matrix",
placement = "top",
trigger = "hover"),
checkboxInput('calneidist_usetumorsamplelabel', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use tumor sample label'),value = FALSE, width = 400),
bsTooltip(id = "calneidist_usetumorsamplelabel",
title = "Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Label'.",
placement = "top",
trigger = "hover"),
# tags$table(
# tags$tr(id = "inline",
# width = "100%",
# tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Title: ")),
# tags$td(width = "70%", textInput(inputId = "calneidist_title", value = NULL, label = NULL)))
# ),
# bsTooltip(id = "calneidist_title",
# title = "The title of the plot.",
# placement = "top",
# trigger = "hover"),
# br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "number.cex")),
tags$td(width = "50%", textInput(inputId = "calneidist_numbercex", value = 8, label = NULL)))
),
bsTooltip(id = "calneidist_numbercex",
title = "The size of text shown in correlation plot. Default 8.",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "number.col")),
tags$td(width = "50%", textInput(inputId = "calneidist_numbercol", value = "#C77960", label = NULL)))
),
bsTooltip(id = "calneidist_numbercol",
title = "The color of text shown in correlation plot. Default #C77960.",
placement = "top",
trigger = "hover"),
br(),
sliderInput(inputId='calneidist_width',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image width'),min = 400,max = 1000, value = 560, width = 500),
sliderInput(inputId='calneidist_height',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image height'),min = 400,max = 1000, value = 560, width = 500),
br(),
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit_calneidist", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
)
)
),
column(
width = 9,
box(
width = NULL,
div(strong("ITH evaluation"),style = "font-size:27px; font-weight:500;"),
p("Understanding the origin and development of intra-tumor heterogeneity is clinically important, which has the potential to yield insights to guide therapeutic strategies. MesKit has integrated several metrics to estimate ITH within region or between regions borrowed from published research and population genetics.",
style = "font-size:20px; font-weight:500;line-height:40px;"),
tabBox(
id = 'tith',
height = "100%",
width = "100%",
selected = "ith_mathscore",
side = "left",
tabPanel(
title = div(icon("chart-bar"), "MATH score", style = "font-size:1.5em; font-weight:600; "),
value = "ith_mathscore",
uiOutput("mathscore.patientlist"),
DT::dataTableOutput('mathScore'),
br(),
br(),
uiOutput("msdb")
),
tabPanel(
title = div(icon("image"), "Mut clustering", style = "font-size:1.5em; font-weight:600; "),
value = "ith_vafcluster",
uiOutput("vafcluster.patientlist"),
uiOutput("vafcluster_table_ui"),
uiOutput("vafcluster.samplelist"),
div(plotOutput("vaf",height = "100%", width = "100%"),align = "left"),
br(),
uiOutput("vcdb")
),
tabPanel(
title = div(icon("image"), "AUC of CCF", style = "font-size:1.5em; font-weight:600; "),
value = "ith_ccfauc",
uiOutput('ccfauc.patientlist'),
uiOutput("ccfauc_table_ui"),
div(plotOutput("ccfauc_plot",height = "100%", width = "100%"),align = "left") ,
uiOutput("ccfauc_db_ui")
),
tabPanel(
title = div(icon("image"), "Fixation index", style = "font-size:1.5em; font-weight:600; "),
value = "ith_calfst",
uiOutput('calfst.patientlist'),
uiOutput("calfst_pair_table_ui"),
div(plotOutput("calfst_plot",height = "100%", width = "100%"),align = "left") ,
uiOutput("calfst_db_ui")
# uiOutput("calfst_avg_table_ui"),
),
tabPanel(
title = div(icon("image"), "Nei's distance", style = "font-size:1.5em; font-weight:600; "),
value = "caInput_calneidist",
uiOutput('calneidist.patientlist'),
uiOutput("calneidist_pair_table_ui"),
div(plotOutput("calneidist_plot",height = "100%", width = "100%"),align = "left") ,
uiOutput("calneidist_db_ui")
# uiOutput("calneidist_avg_table_ui"),
),
tabPanel(
title = div(icon("image"), "Heatmap", style = "font-size:1.5em; font-weight:600; "),
value = "ith_mutheatmap",
uiOutput('mutheatmap.patientlist'),
div(plotOutput("mutheatmap_plot",height = "100%", width = "100%"),align = "left") ,
uiOutput("mutheatmap_db_ui")
)
)
)
)
)
)
bodyAL <- tabItem("AL",
fluidRow(
column(
width = 3,
box(
width = NULL,
conditionalPanel(
condition = "input.al_tabbox == 'pannel_plotmutprofile'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
uiOutput("plotmutprofile.patientlist"),
selectInput("plotmutprofile_class", label = div(style = "font-size:1.5em; font-weight:600; ", "Class"),
choices = c("SP","CS","SPCS"),
selected = "SP"),
bsTooltip(id = "plotmutprofile_class",
title = 'The class which would be represented, default is "SP" (Shared pattern: Public/Shared/Private),other options: "CS" (Clonal status: Clonal/Subclonl) and "SPCS".',
placement = "top",
trigger = "hover"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "Top genes count")),
tags$td(width = "40%", textInput(inputId = "plotmutprofile_topGenesCount", value = 10, label = NULL)))
),
bsTooltip(id = "plotmutprofile_topGenesCount",
title = "The number of genes print, default is 10",
placement = "top",
trigger = "hover"),
br(),
checkboxInput('plotmutprofile_usegenelist', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Gene list'),value = FALSE,width = 400),
bsTooltip(id = "plotmutprofile_usegenelist",
title = "A list of genes to restrict the analysis. Default NULL.",
placement = "top",
trigger = "hover"),
conditionalPanel(
condition = "input.plotmutprofile_usegenelist == true",
fileInput(inputId = 'plotmutprofile_genelist',
label = div(style = "font-size:1.5em; font-weight:600; ", 'Gene list file'),
placeholder = "Example: IntOGen-DriverGenes_COREAD.tsv",
width = 400)
),
checkboxInput('plotmutprofile_classByTumor', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Class by tumor'),value = FALSE,width = 400),
bsTooltip(id = "plotmutprofile_classByTumor",
title = "FALSE(Default). Define shared pattern of mutations based on tumor types (TRUE) or samples (FALSE)",
placement = "top",
trigger = "hover"),
checkboxInput('plotmutprofile_remove_empty_columns', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Remove empty columns'),value = TRUE,width = 400),
bsTooltip(id = "plotmutprofile_remove_empty_columns",
title = "Whether remove the samples without alterations",
placement = "top",
trigger = "hover"),
checkboxInput('plotmutprofile_remove_empty_rows', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Remove empty rows'),value = TRUE,width = 400),
bsTooltip(id = "plotmutprofile_remove_empty_rows",
title = "Whether remove the genes without alterations.",
placement = "top",
trigger = "hover"),
checkboxInput('plotmutprofile_showColnames', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Show column names'),value = TRUE,width = 400),
bsTooltip(id = "plotmutprofile_showColnames",
title = "TRUE(Default). Show sample names of columns.",
placement = "top",
trigger = "hover"),
checkboxInput('plotmutprofile_usetumorsamplelabel', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use tumor sample label'),value = FALSE, width = 400),
bsTooltip(id = "plotmutprofile_useadjvaf",
title = "Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Label'.",
placement = "top",
trigger = "hover"),
sliderInput('plotmutprofile_width', label = div(style = "font-size:1.5em; font-weight:600; ", 'Image width'), min = 400,max = 1200, value = 900,width = 500),
sliderInput('plotmutprofile_height', label = div(style = "font-size:1.5em; font-weight:600; ", 'Image height'), min = 400,max = 1200, value = 900,width = 500),
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit_plotmutprofile", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
),
conditionalPanel(
condition = "input.al_tabbox == 'pannel_plotcna'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
fileInput(inputId = 'plotcna_segfile',
label = div(style = "font-size:1.5em; font-weight:600;",'Segment file',
tags$button(
Id = "iecontrol_seg",
type = "button",
class = "bttn-material-circle",
class = "btn action-button",
list(tags$img(src = "image/button.png",width = "22px",height = "22px")),
style = " background-position: center;padding:0;margin-bottom:7px;"
)
),
placeholder = "Example: CRC_HZ.seg.txt",
width = 400),
# fileInput(inputId = 'plotcna_segfile',
# label = div(style = "font-size:1.5em; font-weight:600; ",
# 'Segment file'),
# width = 400),
checkboxInput('plotmutprofile_usegisticAmpGenes', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Gistic amplification genes'),value = FALSE,width = 400),
bsTooltip(id = "plotmutprofile_usegisticAmpGenes",
title = "Amplification Genes file generated by GISTIC.",
placement = "top",
trigger = "hover"),
conditionalPanel(
condition = "input.plotmutprofile_usegisticAmpGenes == true",
fileInput(inputId = 'plotcna_gisticAmpGenesFile',
label = '',
placeholder = "Example: LIHC_amp_genes.conf_99.txt",
width = 400)
),
checkboxInput('plotmutprofile_usegisticDelGenes', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Gistic deletion genes'),value = FALSE,width = 400),
bsTooltip(id = "plotmutprofile_usegisticDelGenes",
title = "Deletion Genes file generated by GISTIC.",
placement = "top",
trigger = "hover"),
conditionalPanel(
condition = "input.plotmutprofile_usegisticDelGenes == true",
fileInput(inputId = 'plotcna_gisticDelGenesFile',
label = '',
placeholder = "Example: LIHC_del_genes.conf_99.txt",
width = 400)
),
checkboxInput('plotmutprofile_usegisticAllLesions', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Gistic all lesions'),value = FALSE,width = 400),
bsTooltip(id = "plotmutprofile_usegisticAllLesions",
title = "Information of all lesions generated by GISTIC.",
placement = "top",
trigger = "hover"),
conditionalPanel(
condition = "input.plotmutprofile_usegisticAllLesions == true",
fileInput(inputId = 'plotcna_gisticAllLesionsFile',
label = '',
placeholder = "Example: LIHC_all_lesions.conf_99.txt",
width = 400)
),
selectInput('plotcna_refBuild', label = div(style = "font-size:1.5em; font-weight:600; ", 'Genome reference'),
choices = c('hg18','hg19','hg38'),selected = "hg19", width = 400),
bsTooltip(id = "plotcna_refBuild",
title = "Human reference genome versions of hg18, hg19 or hg38 by UCSC. Default: hg19.",
placement = "top",
trigger = "hover"),
uiOutput("plotcna_gistic_parameters_ui"),
br(),
uiOutput("plotcna.patientlist"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "Sample text size")),
tags$td(width = "40%", textInput(inputId = "plotcna_sampletextsize", value = 11, label = NULL)))
),
bsTooltip(id = "plotcna_sampletextsize",
title = "Size of sample name.Default 11.",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "Legend text size")),
tags$td(width = "40%", textInput(inputId = "plotcna_legendtextsize", value = 9, label = NULL)))
),
bsTooltip(id = "plotcna_legendtextsize",
title = "Size of legend text.Default 9.",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "Legend title size")),
tags$td(width = "40%", textInput(inputId = "plotcna_legendtitlesize", value = 11, label = NULL)))
),
bsTooltip(id = "plotcna_legendtitlesize",
title = "Size of legend title.Default 11.",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "Sample bar size")),
tags$td(width = "40%", textInput(inputId = "plotcna_samplebarheight", value = 0.5, label = NULL)))
),
bsTooltip(id = "plotcna_samplebarheight",
title = "Bar height of each sample.Default 0.5.",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "70%", div(style = "font-size:1.5em; font-weight:600; ", "Chromosome bar size")),
tags$td(width = "30%", textInput(inputId = "plotcna_chrombarheight", value = 0.5, label = NULL)))
),
bsTooltip(id = "plotcna_chrombarheight",
title = "Bar height of each chromosome.Default 0.5.",
placement = "top",
trigger = "hover"),
br(),
checkboxInput('plotcna_showrownames',label = div(style = "font-size:1.5em; font-weight:600;padding-left:15px ", 'Show row names'),value = TRUE),
checkboxInput('plotcna_usetumorsamplelabel', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use tumor sample label'),value = FALSE, width = 400),
bsTooltip(id = "plotcna_usetumorsamplelabel",
title = "Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Label'.",
placement = "top",
trigger = "hover"),
checkboxInput('plotcna_removeempytchr', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Remove empty chromosome'),value = FALSE, width = 400),
bsTooltip(id = "plotcna_removeempytchr",
title = "Remove empty chromosomes that do not exist in samples. Default TRUE. ",
placement = "top",
trigger = "hover"),
sliderInput('plotcna_width', label = div(style = "font-size:1.5em; font-weight:600; ", 'Image width'), min = 400,max = 1200, value = 800,width = 500),
sliderInput('plotcna_height', label = div(style = "font-size:1.5em; font-weight:600; ", 'Image height'), min = 400,max = 1200, value = 800,width = 500),
br(),
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit_plotcna", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
),
)
),
column(
width = 9,
box(
width = NULL,
div(strong("Mutational landscape"),style = "font-size:27px; font-weight:500;"),
p("",
style = "font-size:20px; font-weight:500;line-height:40px;"),
tabBox(
id = 'al_tabbox',
selected = 'pannel_plotmutprofile',
side = 'left',
height = "100%",
width = "100%",
tabPanel(
value = 'pannel_plotmutprofile',
title = div(icon("image"), "Mutational profile",style = "font-size:1.5em; font-weight:600; "),
div(plotOutput('plotmutprofile_plot', height = "100%", width = "100%"), align = "left"),
br(),
uiOutput("plotmutprofile_download_button_ui")
),
tabPanel(
value = 'pannel_plotcna',
title = div(icon("image"), "CNA profile", style = "font-size:1.5em; font-weight:600; "),
uiOutput("ie_seg"),
uiOutput("plotcna_table_ui"),
div(plotOutput('plotcna_plot', height = "100%", width = "100%"), align = "left"),
br(),
uiOutput("plotcna_download_button_ui")
)
)
)
)
)
)
bodyclone <- tabItem('clone',
fluidRow(
column(
width = 3,
box(
width = NULL,
conditionalPanel(
condition = "input.clt == 'clone_compareccf'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
uiOutput("compareccf_patientid_ui"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min ccf")),
tags$td(width = "60%", textInput(inputId = "compareccf_minccf", value = 0, label = NULL)))
),
br(),
bsTooltip(id = "compareccf_minccf",
title = "The minimum value of ccf",
placement = "top",
trigger = "hover"),
checkboxInput('compareccf_usetumorsamplelabel', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use tumor sample label'),value = FALSE, width = 400),
bsTooltip(id = "compareccf_usetumorsamplelabel",
title = "Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Label'.",
placement = "top",
trigger = "hover"),
uiOutput("compareccf_pairbytumor_ui"),
# checkboxInput('compareccf_pairbytumor',
# value = FALSE,
# label = div(style = "font-size:1.5em; font-weight:600; padding-left:12px", 'Pair by tumor'),
# width = 500),
# bsTooltip(id = "compareccf_pairbytumor",
# title = "Compare CCF by tumor",
# placement = "top",
# trigger = "hover"),
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit_compareccf", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
),
conditionalPanel(
condition = "input.clt == 'clone_caljsi'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
uiOutput("caljsi_patientid_ui"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min ccf")),
tags$td(width = "60%", textInput(inputId = "caljsi_minccf", value = 0, label = NULL)))
),
bsTooltip(id = "caljsi_minccf",
title = "The minimum value of ccf",
placement = "top",
trigger = "hover"),
checkboxInput('caljsi_usetumorsamplelabel', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use tumor sample label'),value = FALSE, width = 400),
bsTooltip(id = "caljsi_usetumorsamplelabel",
title = "Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Label'.",
placement = "top",
trigger = "hover"),
uiOutput("caljsi_pairbytumor_ui"),
# checkboxInput('caljsi_pairbytumor',
# value = FALSE,
# label = div(style = "font-size:1.5em; font-weight:600; padding-left:12px", 'Pair by tumor'),
# width = 500),
# bsTooltip(id = "caljsi_pairbytumor",
# title = "calculate JSI by tumor",
# placement = "top",
# trigger = "hover"),
checkboxInput('caljsi_usecircle',
value = TRUE,
label = div(style = "font-size:1.5em; font-weight:600; padding-left:12px", 'Use circle'),
width = 500),
bsTooltip(id = "caljsi_usecircle",
title = "Logical (Default:TRUE). Whether to use circle as visualization method of correlation matrix",
placement = "top",
trigger = "hover"),
# tags$table(
# tags$tr(id = "inline",
# width = "100%",
# tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Title: ")),
# tags$td(width = "70%", textInput(inputId = "caljsi_title", value = NULL, label = NULL)))
# ),
# bsTooltip(id = "caljsi_title",
# title = "The title of the plot.",
# placement = "top",
# trigger = "hover"),
# br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "number.cex")),
tags$td(width = "40%", textInput(inputId = "caljsi_numbercex", value = 8, label = NULL)))
),
bsTooltip(id = "caljsi_numbercex",
title = "The size of text shown in correlation plot. Default 8.",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "number.col")),
tags$td(width = "40%", textInput(inputId = "caljsi_numbercol", value = "#C77960", label = NULL)))
),
bsTooltip(id = "caljsi_numbercol",
title = "The color of text shown in correlation plot. Default #C77960.",
placement = "top",
trigger = "hover"),
br(),
sliderInput(inputId='caljsi_width',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image width'),min = 400,max = 1000, value = 560, width = 500),
sliderInput(inputId='caljsi_height',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image height'),min = 400,max = 1000, value = 560, width = 500),
br(),
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit_caljsi", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
),
conditionalPanel(
condition = "input.clt == 'clone_testneutral'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
uiOutput("testneutral_patientid_ui"),
checkboxInput('testneutral_withintumor',div(style = "font-size:1.5em; font-weight:600; padding-left:15px ", 'Within Tumor'),value = FALSE),
bsTooltip(id = "testneutral_withintumor",
title = 'Test neutral within tumros in each patients,default is FALSE.',
placement = "top",
trigger = "hover"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "Min total depth: ")),
tags$td(width = "50%", textInput(inputId = "testneutral_mintotaldepth", value = 2, label = NULL)))
),
bsTooltip(id = "testneutral_mintotaldepth",
title = "The minimun total depth of coverage. Defalut: 2",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min vaf: ")),
tags$td(width = "70%", textInput(inputId = "testneutral_minvaf", value = 0.1, label = NULL)))
),
bsTooltip(id = "testneutral_minvaf",
title = "The minimum value of vaf",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Max vaf: ")),
tags$td(width = "70%", textInput(inputId = "testneutral_maxvaf", value = 0.3, label = NULL)))
),
bsTooltip(id = "testneutral_maxvaf",
title = "The maximum value of vaf",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "R2 threshold: ")),
tags$td(width = "50%", textInput(inputId = "testneutral_R2threshold", value = 0.98, label = NULL)))
),
bsTooltip(id = "testneutral_R2threshold",
title = "The threshod of R2 to decide whether a tumor follows neutral evolution. Default: 0.98",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "Min mut count: ")),
tags$td(width = "50%", textInput(inputId = "testneutral_minmutcount", value = 20, label = NULL)))
),
bsTooltip(id = "testneutral_minmutcount",
title = "The minimun number of subclonal mutations used to fit model. Default: 20",
placement = "top",
trigger = "hover"),
br(),
sliderInput(inputId='testneutral_width',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image width'),min = 400,max = 1000, value = 560, width = 500),
sliderInput(inputId='testneutral_height',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image height'),min = 400,max = 1000, value = 560, width = 500),
br(),
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit_testneutral", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
)
)
),
column(
width = 9,
box(
width = NULL,
div(strong("Metastatic routes inference"),style = "font-size:27px; font-weight:500;"),
p("Since metastasis is the ultimate cause of death for most patients, it is particularly important to gain a systematic understanding of how tumor disseminates and the scale of ongoing parallel evolution in metastatic and primary site. Here, we provide two functions to help distinguish monoclonal from polyclonal seeding. ",
style = "font-size:20px; font-weight:500;line-height:40px;"),
tabBox(
id = 'clt',
selected = 'clone_compareccf',
side = 'left',
height = "100%",
width = "100%",
tabPanel(
value = 'clone_compareccf',
title = div(icon("chart-bar"), "CCF comparison", style = "font-size:1.5em; font-weight:600; "),
uiOutput('compareccf.patientlist'),
uiOutput('compareccf.samplelist'),
br(),
uiOutput("compareccf_table_ui")
),
tabPanel(
title = div(icon("image"), "Jaccard similarity index", style = "font-size:1.5em; font-weight:600; "),
value = "clone_caljsi",
uiOutput('caljsi.patientlist'),
uiOutput("caljsi_pair_table_ui"),
br(),
div(plotOutput("caljsi_plot",height = "100%", width = "100%"),align = "left") ,
uiOutput("caljsi_db_ui")
)
# tabPanel(
# title = div(icon("box"), "testNeutral"),
# value = "clone_testneutral",
# uiOutput('testneutral.patientlist'),
# uiOutput("testneutral_table_ui"),
# br(),
# uiOutput('testneutral.samplelist'),
# uiOutput('warningMessage_testneutral'),
# div(plotOutput("testneutral_plot",height = "100%", width = "100%"),align = "center") ,
# uiOutput("testneutral_db_ui")
# )
)
)
)
)
)
bodytree <- tabItem('tree',
fluidRow(
column(
width = 3,
box(
width = NULL,
# conditionalPanel(
# condition = "input.sgt == 'S_getphylotree'",
# div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
# br(),
# selectInput("getphylotree_method", label = div(style = "font-size:1.5em; font-weight:600; ", "Tree construct method"),
# choices = c("NJ","MP","ML","FASTME.ols","FASTME.bal"),
# selected = "NJ"),
# bsTooltip(id = "getphylotree_method",
# title = "Approach to construct phylogenetic trees",
# placement = "top",
# trigger = "hover"),
# tags$table(
# tags$tr(id = "inline",
# width = "100%",
# tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min vaf: ")),
# tags$td(width = "70%", textInput(inputId = "getphylotree_minvaf", value = 0.02, label = NULL)))
# ),
# bsTooltip(id = "getphylotree_minvaf",
# title = "The minimum value of vaf",
# placement = "top",
# trigger = "hover"),
# br(),
# tags$table(
# tags$tr(id = "inline",
# width = "100%",
# tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min ccf: ")),
# tags$td(width = "70%", textInput(inputId = "getphylotree_minccf", value = 0, label = NULL)))
# ),
# bsTooltip(id = "getphylotree_minccf",
# title = "The minimum value of ccf",
# placement = "top",
# trigger = "hover"),
# br(),
# tags$table(
# tags$tr(id = "inline",
# width = "100%",
# tags$td(width = "60%", div(style = "font-size:1.5em; font-weight:600; ", "Boostrap repetitions: ")),
# tags$td(width = "40%", textInput(inputId = "getphylotree_bootstraprepnum", value = 100, label = NULL)))
# ),
# bsTooltip(id = "getphylotree_bootstraprepnum",
# title = "Bootstrap iterations. Default 100.",
# placement = "top",
# trigger = "hover"),
# br(),
# actionBttn('submit_getphylotree',div(
# strong("Get phylotree"),align = 'center'))
# ),
conditionalPanel(
condition = "input.sgt == 'S_plotphylotree'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
uiOutput("plotphylotree_patientid_ui"),
selectInput("plotphylotree_getphylotree_method", label = div(style = "font-size:1.5em; font-weight:600; ", "Tree construct method"),
choices = c("NJ","MP","ML","FASTME.ols","FASTME.bal"),
selected = "NJ"),
bsTooltip(id = "plotphylotree_getphylotree_method",
title = "Approach to construct phylogenetic trees",
placement = "top",
trigger = "hover"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min vaf")),
tags$td(width = "60%", textInput(inputId = "plotphylotree_getphylotree_minvaf", value = 0, label = NULL)))
),
bsTooltip(id = "plotphylotree_getphylotree_minvaf",
title = "The minimum value of vaf",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min ccf")),
tags$td(width = "60%", textInput(inputId = "plotphylotree_getphylotree_minccf", value = 0, label = NULL)))
),
bsTooltip(id = "plotphylotree_getphylotree_minccf",
title = "The minimum value of ccf",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "Boostrap repetitions")),
tags$td(width = "30%", textInput(inputId = "plotphylotree_getphylotree_bootstraprepnum", value = 100, label = NULL)))
),
bsTooltip(id = "plotphylotree_getphylotree_bootstraprepnum",
title = "Bootstrap iterations. Default 100.",
placement = "top",
trigger = "hover"),
br(),
selectInput("plotphylotree_branchcol", label = div(style = "font-size:1.5em; font-weight:600; ", "Branch color"),
choices = c("mutType",
"mutSig",
"NULL"),
selected = "mutType"),
bsTooltip(id = "plotphylotree_branchcol",
title = "Specify the colors of branches (Default: mutType). Other options: 'mutSig' for coloring branches by branch mutation signature;",
placement = "top",
trigger = "hover"),
conditionalPanel(
condition = "input.plotphylotree_branchcol == 'mutSig'",
selectInput("plotphylotree_signatureref", label = div(style = "font-size:1.5em; font-weight:600; ", "Signautre reference"),
choices = c("cosmic_v2",
"nature2013",
"exome_cosmic_v3"),
selected = "cosmic_v2"),
bsTooltip(id = "plotphylotree_signatureref",
title = 'signature reference',
placement = "top",
trigger = "hover"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "60%", div(style = "font-size:1.5em; font-weight:600; ", "Minimal mutation number")),
tags$td(width = "20%", textInput(inputId = "plotphylotree_minmutcount", value = 15, label = NULL)))
),
bsTooltip(id = "plotphylotree_minmutcount",
title = 'The threshold for the variants in a branch. Default 15.',
placement = "top",
trigger = "hover"),
),
checkboxInput('plotphylotree_showbootstrap',div(style = "font-size:1.5em; font-weight:600; padding-left:15px ", 'Show bootstrap value'),value = TRUE),
bsTooltip(id = "plotphylotree_showbootstrap",
title = 'Whether to add bootstrap value on internal nodes.',
placement = "top",
trigger = "hover"),
checkboxInput('plotphylotree_usetumorsamplelabel', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use tumor sample label'),value = FALSE, width = 400),
bsTooltip(id = "plotphylotree_usetumorsamplelabel",
title = "Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Label'.",
placement = "top",
trigger = "hover"),
checkboxInput('plotphylotree_show_scale_bar', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Show scale bar'),value = FALSE, width = 400),
bsTooltip(id = "plotphylotree_show_scale_bar",
title = "Logical (Default: FALSE). Whether to show scale bar.This function adds a horizontal bar giving the scale of the branch lengths to a plot on the current graphical device.",
placement = "top",
trigger = "hover"),
conditionalPanel(
condition = "input.plotphylotree_show_scale_bar == true",
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Scale bar x")),
tags$td(width = "60%", textInput(inputId = "plotphylotree_scale_bar_x", value = NULL, label = NULL)))
),
bsTooltip(id = "plotphylotree_scale_bar_x",
title = "The x location of scale bar.",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Scale bar y")),
tags$td(width = "60%", textInput(inputId = "plotphylotree_scale_bar_y", value = NULL, label = NULL)))
),
bsTooltip(id = "plotphylotree_scale_bar_y",
title = "The y location of scale bar.",
placement = "top",
trigger = "hover"),
br(),
),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min ratio")),
tags$td(width = "60%", textInput(inputId = "plotphylotree_minratio", value = 0.05, label = NULL)))
),
bsTooltip(id = "plotphylotree_minratio",
title = "Double (Default:1/20). If min.ratio is not NULL,all edge length of a phylogenetic tree should be greater than min.ratio*the longest edge length.If not, the edge length will be reset as min.ratio*longest edge length.",
placement = "top",
trigger = "hover"),
br(),
sliderInput(inputId='plotphylotree_width',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image width'),min = 300,max = 1200, value = 500, width = 500),
sliderInput(inputId='plotphylotree_height',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image height'),min = 300,max = 1200, value = 500, width = 500),
#
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit_plotphylotree", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
),
conditionalPanel(
condition = "input.sgt == 'S_comparetree'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
uiOutput("comparetree.patientlist"),
selectInput("comparetree_getphylotree_method1",
label = div(style = "font-size:1.5em; font-weight:600; ",
"Tree1 construct method"),
choices = c("NJ","MP","ML","FASTME.ols","FASTME.bal"),
selected = "NJ"),
bsTooltip(id = "comparetree_getphylotree_method1",
title = "Approach to construct phylogenetic trees",
placement = "top",
trigger = "hover"),
selectInput("comparetree_getphylotree_method2",
label = div(style = "font-size:1.5em; font-weight:600; ",
"Tree2 construct method"),
choices = c("NJ","MP","ML","FASTME.ols","FASTME.bal"),
selected = "MP"),
bsTooltip(id = "comparetree_getphylotree_method2",
title = "Approach to construct phylogenetic trees",
placement = "top",
trigger = "hover"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min vaf")),
tags$td(width = "60%", textInput(inputId = "comparetree_getphylotree_minvaf", value = 0, label = NULL)))
),
bsTooltip(id = "comparetree_getphylotree_minvaf",
title = "The minimum value of vaf",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min ccf")),
tags$td(width = "60%", textInput(inputId = "comparetree_getphylotree_minccf", value = 0, label = NULL)))
),
bsTooltip(id = "comparetree_getphylotree_minccf",
title = "The minimum value of ccf",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%",
div(style = "font-size:1.5em; font-weight:600; ",
"Boostrap repetitions")),
tags$td(width = "30%",
textInput(inputId = "comparetree_getphylotree_bootstraprepnum",
value = 100, label = NULL)))
),
bsTooltip(id = "comparetree_getphylotree_bootstraprepnum",
title = "Bootstrap iterations. Default 100.",
placement = "top",
trigger = "hover"),
br(),
# div(strong("Parameter(phyloTree2)"),style = "font-size:1.6em; font-weight:600;"),
# selectInput("comparetree_getphylotree_method2", label = div(style = "font-size:1.5em; font-weight:600; ", "Tree construct method"),
# choices = c("NJ","MP","ML","FASTME.ols","FASTME.bal"),
# selected = "MP"),
# bsTooltip(id = "comparetree_getphylotree_method2",
# title = "Approach to construct phylogenetic trees",
# placement = "top",
# trigger = "hover"),
# tags$table(
# tags$tr(id = "inline",
# width = "100%",
# tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min vaf: ")),
# tags$td(width = "70%", textInput(inputId = "comparetree_getphylotree_minvaf2", value = 0.02, label = NULL)))
# ),
# bsTooltip(id = "comparetree_getphylotree_minvaf2",
# title = "The minimum value of vaf",
# placement = "top",
# trigger = "hover"),
# br(),
# tags$table(
# tags$tr(id = "inline",
# width = "100%",
# tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min ccf: ")),
# tags$td(width = "70%", textInput(inputId = "comparetree_getphylotree_minccf2", value = 0, label = NULL)))
# ),
# bsTooltip(id = "comparetree_getphylotree_minccf2",
# title = "The minimum value of ccf",
# placement = "top",
# trigger = "hover"),
# br(),
# tags$table(
# tags$tr(id = "inline",
# width = "100%",
# tags$td(width = "60%", div(style = "font-size:1.5em; font-weight:600; ", "Boostrap repetitions: ")),
# tags$td(width = "40%", textInput(inputId = "comparetree_getphylotree_bootstraprepnum2", value = 100, label = NULL)))
# ),
# bsTooltip(id = "comparetree_getphylotree_bootstraprepnum2",
# title = "Bootstrap iterations. Default 100.",
# placement = "top",
# trigger = "hover"),
# br(),
# div(strong("Parameter(compareTree)"),style = "font-size:1.6em; font-weight:600;"),
checkboxInput('comparetree_showbootstrap',
div(style = "font-size:1.5em; font-weight:600; padding-left:15px ",
'Show bootstrap value'),value = FALSE),
bsTooltip(id = "comparetree_showbootstrap",
title = 'Whether to add bootstrap value on internal nodes.',
placement = "top",
trigger = "hover"),
checkboxInput('comparetree_usetumorsamplelabel', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use tumor sample label'),value = FALSE, width = 400),
bsTooltip(id = "comparetree_usetumorsamplelabel",
title = "Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Label'.",
placement = "top",
trigger = "hover"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min ratio")),
tags$td(width = "60%", textInput(inputId = "comparetree_minratio", value = 0.05, label = NULL)))
),
bsTooltip(id = "comparetree_minratio",
title = "Double (Default:1/20). If min.ratio is not NULL,all edge length of a phylogenetic tree should be greater than min.ratio*the longest edge length.If not, the edge length will be reset as min.ratio*longest edge length.",
placement = "top",
trigger = "hover"),
br(),
# textInput(inputId = "comparetree_commoncol",
# label = div(style = "font-size:1.5em; font-weight:600; ", 'Common color'),
# value = "red"),
# bsTooltip(id = "comparetree_commoncol",
# title = "Color of common branches.",
# placement = "right",
# trigger = "hover"),
sliderInput(inputId='comparetree_width',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image width'),min = 700,max = 1400, value = 1100, width = 500),
sliderInput(inputId='comparetree_height',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image height'),min = 400,max = 1000, value = 700, width = 500),
#
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit_comparetree", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
),
conditionalPanel(
condition = "input.sgt == 'S_treemutsig'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
uiOutput("treemutsig_patientid_ui"),
selectInput("treemutsig_getphylotree_method", label = div(style = "font-size:1.5em; font-weight:600; ", "Tree construct method"),
choices = c("NJ","MP","ML","FASTME.ols","FASTME.bal"),
selected = "NJ"),
bsTooltip(id = "treemutsig_getphylotree_method",
title = "Approach to construct phylogenetic trees",
placement = "top",
trigger = "hover"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min vaf")),
tags$td(width = "60%", textInput(inputId = "treemutsig_getphylotree_minvaf", value = 0, label = NULL)))
),
bsTooltip(id = "treemutsig_getphylotree_minvaf",
title = "The minimum value of vaf",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min ccf")),
tags$td(width = "60%", textInput(inputId = "treemutsig_getphylotree_minccf", value = 0, label = NULL)))
),
bsTooltip(id = "treemutsig_getphylotree_minccf",
title = "The minimum value of ccf",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "Boostrap repetitions")),
tags$td(width = "30%", textInput(inputId = "treemutsig_getphylotree_bootstraprepnum", value = 100, label = NULL)))
),
bsTooltip(id = "treemutsig_getphylotree_bootstraprepnum",
title = "Bootstrap iterations. Default 100.",
placement = "top",
trigger = "hover"),
br(),
selectInput('treemutsig_level', label = div(style = "font-size:1.5em; font-weight:600; ", 'Level'),
choices = c('1','2','3', '4', '5', '6'),selected = "2", width = 400),
bsTooltip(id = "treemutsig_level",
title = " Calculate mutation in different levels.'1': patient,'2':tumor,'3':sample,'4':branch,'5':mutation type.Default level '2'.",
placement = "top",
trigger = "hover"),
# checkboxInput('treemutsig_withintumor',label = div(style = "font-size:1.5em; font-weight:600;padding-left:15px ", 'Within tumor'),value = FALSE),
# bsTooltip(id = "treemutsig_withintumor",
# title = 'Exploring signatures within tumor. Default: FALSE.',
# placement = "top",
# trigger = "hover"),
selectInput("treemutsig_signatureref", label = div(style = "font-size:1.5em; font-weight:600; ", "Signautre reference"),
choices = c("cosmic_v2",
"nature2013",
"exome_cosmic_v3"),
selected = "cosmic"),
bsTooltip(id = "treemutsig_signatureref",
title = 'signature reference',
placement = "top",
trigger = "hover"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "85%", div(style = "font-size:1.5em; font-weight:600; ", "Minimal mutation number")),
tags$td(width = "15%", textInput(inputId = "treemutsig_minmutcount", value = 15, label = NULL)))
),
bsTooltip(id = "treemutsig_minmutcount",
title = 'The threshold for the variants in a branch. Default 15.',
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "Signature cutoff")),
tags$td(width = "30%", textInput(inputId = "treemutsig_signaturecutoff", value = 0.1, label = NULL)))
),
bsTooltip(id = "treemutsig_signaturecutoff",
title = 'Discard any signature contributions with a weight less than this amount.Default: 0.1.',
placement = "top",
trigger = "hover"),
br(),
selectInput("treemutsig_mode", label = div(style = "font-size:1.5em; font-weight:600; ", "Mode"),
choices = c('NULL',
'Original',
'Reconstructed',
'Difference'),
selected = "NULL"),
bsTooltip(id = "treemutsig_mode",
title = "type of mutation spectrum.Default: NULL. Options:'Original','Reconstructed' or 'Difference'",
placement = "top",
trigger = "hover"),
checkboxInput('treemutsig_usetumorsamplelabel', label = div(style = "font-size:1.5em; font-weight:600; padding-left:15px", 'Use tumor sample label'),value = FALSE, width = 400),
bsTooltip(id = "treemutsig_usetumorsamplelabel",
title = "Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Label'.",
placement = "top",
trigger = "hover"),
sliderInput(inputId='treemutsig_width',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image width'),min = 400,max = 1000, value = 800, width = 500),
sliderInput(inputId='treemutsig_height',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image height'),min = 400,max = 1000, value = 560, width = 500),
br(),
br(),
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit_treemutsig", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
),
conditionalPanel(
condition = "input.sgt == 'S_muttrunkbranch'",
div(strong("Parameter"),style = "font-size:2em; font-weight:600;"),
br(),
uiOutput("muttrunkbranch_patientid_ui"),
selectInput("muttrunkbranch_getphylotree_method", label = div(style = "font-size:1.5em; font-weight:600; ", "Tree construct method"),
choices = c("NJ","MP","ML","FASTME.ols","FASTME.bal"),
selected = "NJ"),
bsTooltip(id = "muttrunkbranch_getphylotree_method",
title = "Approach to construct phylogenetic trees",
placement = "top",
trigger = "hover"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min vaf")),
tags$td(width = "60%", textInput(inputId = "muttrunkbranch_getphylotree_minvaf", value = 0, label = NULL)))
),
bsTooltip(id = "muttrunkbranch_getphylotree_minvaf",
title = "The minimum value of vaf",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "Min ccf")),
tags$td(width = "60%", textInput(inputId = "muttrunkbranch_getphylotree_minccf", value = 0, label = NULL)))
),
bsTooltip(id = "muttrunkbranch_getphylotree_minccf",
title = "The minimum value of ccf",
placement = "top",
trigger = "hover"),
br(),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "50%", div(style = "font-size:1.5em; font-weight:600; ", "Boostrap repetitions")),
tags$td(width = "30%", textInput(inputId = "muttrunkbranch_getphylotree_bootstraprepnum", value = 100, label = NULL)))
),
bsTooltip(id = "muttrunkbranch_getphylotree_bootstraprepnum",
title = "Bootstrap iterations. Default 100.",
placement = "top",
trigger = "hover"),
checkboxInput('muttrunkbranch_ct',div(style = "font-size:1.5em; font-weight:600; padding-left:15px ", 'CT'),value = FALSE),
bsTooltip(id = "muttrunkbranch_ct",
title = 'Distinction between C>T at CpG and C>T at other sites, Default FALSE',
placement = "top",
trigger = "hover"),
tags$table(
tags$tr(id = "inline",
width = "100%",
tags$td(width = "30%", div(style = "font-size:1.5em; font-weight:600; ", "P-value")),
tags$td(width = "60%", textInput(inputId = "muttrunkbranch_pvalue", value = 0.05, label = NULL)))
),
br(),
bsTooltip(id = "muttrunkbranch_pvalue",
title = "Confidence level of the interval for Fisher test. Default: 0.05.",
placement = "right",
trigger = "hover"),
sliderInput(inputId='muttrunkbranch_width',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image width'),min = 400,max = 1000, value = 470, width = 500),
sliderInput(inputId='muttrunkbranch_height',label = div(style = "font-size:1.5em; font-weight:600; ", 'Image height'),min = 400,max = 1000, value = 470, width = 500),
br(),
br(),
fluidRow(
column(
width = 9,
div(
tags$button(
id = "submit_muttrunkbranch", type = "button", class = "action-button bttn",
class = "bttn-unite", class = paste0("bttn-md"),
class = paste0("bttn-default"),
list(strong("Start analysis"),icon("hand-right", lib = "glyphicon")),
style = "margin-bottom:0px;margin-right:0px;"
)
)
)
)
)
)
),
column(
width = 9,
box(
width = NULL,
div(strong("PhyloTree-based analysis"),style = "font-size:27px; font-weight:500;"),
p("Systematic understanding of evolutionary relationship among regions plays a fundamental role in MRS study, where phylogenetic tree is the primary tool for describing these associations and interpreting ITH. MesKit is capable of constructing and comparing phylogenetic trees based on different methods, visualizing the rooted phylogenetic trees with annotation, as well as charactering mutational patterns based on phylogenetic trees.",
style = "font-size:20px; font-weight:500;line-height:40px;"),
tabBox(
id = 'sgt',
side = 'left',
selected = 'S_plotphylotree',
width = "100%",
height = "100%",
tabPanel(
title = div(icon("tree"), "Plot phylotree", style = "font-size:1.5em; font-weight:600; "),
value = 'S_plotphylotree',
uiOutput("phylotree.patientlist"),
div(plotOutput("phylotree_plot",height = "100%",width = "100%"),align = "left"),
br(),
uiOutput("phylotree_downloadbutton_ui")
),
tabPanel(
title = div(icon("tree"), "Compare tree", style = "font-size:1.5em; font-weight:600; "),
value = 'S_comparetree',
verbatimTextOutput("comparetree_dist"),
br(),
div(plotOutput('comparetree_plot', height = "100%", width = "100%"),align = "left"),
uiOutput('comparetree_db_ui')
# br(),
# uiOutput('treemutsig_table_ui')
),
tabPanel(
title = div(icon("image"), "Mutational signature", style = "font-size:1.5em; font-weight:600; "),
value = 'S_treemutsig',
# uiOutput('warningMessage_treemutsig'),
uiOutput("treemutsig.patientlist"),
uiOutput("treemutsig.samplelist"),
div(plotOutput('treemutsig_plot', height = "100%", width = "100%"),align = "left"),
uiOutput("treemutsig_download_button_ui"),
# br(),
# uiOutput('treemutsig_table_ui')
),
tabPanel(
title = div(icon("image"), "MutTrunkBranch", style = "font-size:1.5em; font-weight:600; "),
value = 'S_muttrunkbranch',
uiOutput("muttrunkbranch.patientlist"),
br(),
uiOutput('muttrunkbranch_table_ui'),
div(plotOutput('muttrunkbranch_plot', height = "100%", width = "100%"),align = "left"),
uiOutput("muttrunkbranch_download_button_ui")
)
)
)
)
)
)
#Main function----
dbHeader <- dashboardHeader(title = "MesKit", titleWidth = 300,
# tags$li(class = "dropdown", actionLink(inputId = "help", label = div(style = "font-size:15px; font-weight:400; ", "Help"))),
# tags$li(class = "dropdown", actionLink(inputId = "contact", label = div(style = "font-size:15px; font-weight:400; ", "Contact"))),
dropdownMenu(
type = "notifications",
icon = icon("question-circle"),
badgeStatus = NULL,
headerText = "Help:",
notificationItem("MesKit github page", icon = icon("file"),
href = "https://github.com/Niinleslie/MesKit")
),
dropdownMenu(
type = "notifications",
icon = icon("envelope"),
badgeStatus = NULL,
headerText = "",
tags$li(p("Mengni Liu, liumn5@mail2.sysu.edu.cn")),
tags$li(p("Jianyu Chen, chenjy327@mail2.sysu.edu.cn")),
tags$li(p("Xin Wang, wangx555@mail2.sysu.edu.cn")),
tags$li(p("Chengwei Wang, wangchw8@outlook.com"))
# notificationItem("Mengni Liu, liumn5@mail2.sysu.edu.cn, Sun Yat-sen university", icon = icon("user"),href = "liumn5@mail2.sysu.edu.cn"),
# notificationItem("Chengwei Wang, wangchw8@outlook.com, Sun Yat-sen university", icon = icon("user"),href = "wangchw8@outlook.com"),
# notificationItem("Jianyu Chen, chenjy327@mail2.sysu.edu.cn, Sun Yat-sen university", icon = icon("user"),href = "chenjy327@mail2.sysu.edu.cn"),
# notificationItem("Xin Wang, wangx555@mail2.sysu.edu.cn, Sun Yat-sen university", icon = icon("user"),href = "wangx555@mail2.sysu.edu.cn")
)
)
dbHeader$children[[2]]$children <- tags$a(href='https://github.com/Niinleslie/MesKit',
tags$img(src='image/logo.jpg',height='65',width='250'))
shinyUI(
dashboardPage(
skin = "blue",
header=dbHeader ,
sidebar=sidebar,
body=dashboardBody(
## add text behind the sidebar (design error)
tags$head(tags$style(HTML(
"/* logo */
.skin-blue .main-header .logo {
background-color: #3c8dbc;
}
/* logo when hovered */
.skin-blue .main-header .logo:hover {
background-color: #3c8dbc;
}
.textnvbar {
font-size: 20px;
line-height: 50px;
text-align: left;
font-family: 'Helvetica Neue',Helvetica,Arial,sans-serif;
padding: 0 15px;
overflow: hidden;
color: white;
}
.checkbox { /* checkbox is a div class*/
line-height: 25px;}
input[type='checkbox']{
width: 23px; /*Desired width*/
height: 23px; /*Desired height*/
line-height: 25px;
}
span {
line-height: 30px;
}
"))),
## change the style of the progress bar.
# tags$head(tags$style(
# type="text/css",
# ".progress.shiny-file-input-progress {
# height:5px;
# }
#
# .progress-bar {
# background-image: linear-gradient(to right, #77C7FF, #3c8dbc ) !important;
# background-size: auto !important;
# font-size:0px;
# height:5px;
# }"
# )),
tags$script(HTML('
$(document).ready(function() {
$("header").find("nav").append(\'<span class="textnvbar"> MesKit: A Tool Kit for Dissecting Cancer Evolution of Multi-region Tumor Biopsies through Somatic Alterations</span>\');
})
')),
tags$head(
tags$style(type="text/css", "#inline label{ display: table-cell; text-align: centers; vertical-align: middle; width=400; }
#inline .form-group { display: table-row; width=400; }"),
tags$style(HTML("
.shiny-output-error-validation {
color: brown;
}
.shiny-notification {
height: 200px;
width: 600px;
position:fixed;
font-size: 30px;
top: calc(50% - 100px);
left: calc(50% + 100px);
}
.dt-right {
text-align: justify !important;
}
.shiny-output-error-validation {
color: green;
font-size:27px;
font-weight:500;
}
.main-sidebar { font-size: 20px; }
table.dataTable tbody th, table.dataTable tbody td {
padding: 10px 1.5em !important;
}
.tooltip {
min-width: 15em !important;
}
.progress-message, .progress-detail {
display: block !important;
}
# .shiny-notification-close {
# float: right;/*image size adjust */
# font-weight: bold;
# font-size: 30px;
# bottom: 9px;
# position: relative;
# padding-left: 4px;
# color: #444;
# cursor: default;
# }
# .pipediv{
# width:900px;
# height:500px;
# }
# .pipediv .pipe{
# float:left;
# }
# .pipediv .pipe img{
# width:500px;
# height:500px;
# }
# .pipetext{
#
# }
")),
tags$link(rel = "stylesheet", type = "text/css", href = "main.css")
),
tabItems(
bodyHome,
bodyIP,
bodyAL,
bodyITH,
bodyclone,
# bodyfunction,
bodytree
# bodySurvival
)
)
)
)
Try the MesKit package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.