inst/app/contributions/gQC_generalQC/ui.R
In C3BI-pasteur-fr/UTechSCB-SCHNAPPs: Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data
# gQC_generalQC/ui.R
suppressMessages(require(magrittr))
source(paste0(packagePath, .Platform$file.sep , "modulesUI.R"), local = TRUE)
menuList <- list(
shinydashboard::menuItem("General QC",
# id="generalQCID",
tabName = "generalQC", icon = icon("thumbs-up"), startExpanded = FALSE,
shinydashboard::menuSubItem("UMI histogram", tabName = "gQC_umiHist"),
shinydashboard::menuSubItem("Sample histogram", tabName = "gQC_sampleHist"),
shinydashboard::menuSubItem("PC variance", tabName = "gQC_variancePC"),
if("DoubletFinder" %in% installed.packages()){
shinydashboard::menuSubItem("Doublet Finder", tabName = "gQC_doubletFinder")},
shinydashboard::menuSubItem("Scater QC", tabName = "DE_scaterQC")
# shinydashboard::menuSubItem("TSNE plot", tabName = "gQC_tsnePlot"),
# shinydashboard::menuSubItem("Umap", tabName = "gQC_umapPlot")
)
)
# gQC_doubletFinder ----
if("DoubletFinder" %in% installed.packages()){
DoubletFinderTab <- shinydashboard::tabItem(
tabName = "gQC_doubletFinder",
fluidRow(div(h3("DoubletFinder"), align = "center")),
br(),
tabBox(title = "", width = 12, id = "doubletFinderBox",
tabPanel(
title = "Doublet Finder", solidHeader = TRUE, width = 12, value = "doubletFinderTab",
id = "doublet.Finder.Tab",
fluidRow(
column(
width = 6,
sc_numericInput("GS_DF_dims", "PC imensions to use", min = 0, max = 200, step = 1, value = defaultValue("GS_DF_dims", 20))
),
column(
width = 6,
sc_numericInput("GS_DF_nRecover", "number of cells recovered by CellRanger (before QC)", min = 100, max = 20000000, step = 1000, value = defaultValue("GS_DF_nRecover", 10000))
)
),
fluidRow(
column(
width = 6,
sc_numericInput("GS_DF_pk", "neighborhood size to estimate likelihood of being doublet \n
(expressed as fraction of merged real-artifical data)", min = 0, max = Inf, step = 1, value = defaultValue("GS_DF_pk", 20))
),
column(
width = 6,
sc_numericInput("GS_DF_pN", "number of artificial doublets generated \n
(expressed as fraction of merged real-artifical data)", min = 0, max = 1, step = 0.01, value = defaultValue("GS_DF_pN", 0.10))
)
),
br(),
fluidRow(
column(
width = 12, offset = 1,
actionButton("GS_DF_button", "apply changes", width = "80%")
)
),
fluidRow(
column(
width = 12,
clusterUI("GS_DF_plot")
)
)
)
)
)
}
# geneSetModTab -----
geneSetModTab <- shinydashboard::tabItem(
tabName = "modifyGeneSets",
fluidRow(div(h3("work with gene sets"), align = "center")),
br(),
tabBox(title = "modify gene sets", width = 12, id = "modGS",
tabPanel(
title = "Rename gene set", solidHeader = TRUE, width = 12, value = "renameGS",
id = "rename.GS.Tab",
fluidRow(
column(
width = 6,
sc_selectInput("oldGS", "gene sets to copy + rename", choices = defaultValue("oldGS", "notyet"), selected = defaultValue("oldGS", "notyet")),
verbatimTextOutput("gQC_renameGenes") %>% jqui_resizable()
),
column(
width = 6,
fluidRow(
column(
width = 8,
sc_textInput("newGS", "new name of gene set", value = defaultValue("newGS", ""))
),
column(
width = 4,
actionButton("updateGSButton", "rename")
)
),
fluidRow(
column(
width = 8,
sc_selectInput("delGS", "gene set to delete", choices = defaultValue("delGS", "notyet"), selected = defaultValue("delGS", "notyet"))
),
column(
width = 4,
actionButton("delGSButton", "delete")
),
tags$style(type = "text/css", "#updateGSButton { width:100%; margin-top: 25px;}"),
tags$style(type = "text/css", "#delGSButton { width:100%; margin-top: 25px;}")
)
)
)
),
tabPanel(
title = "edit gene set", solidHeader = TRUE, width = 12, value = "gQC_editGS",
id = "gQC_editGS.Tab",
tags$p("Select a gene set and then edit it"),
fluidRow(
column(
width = 12,
sc_selectizeInput(inputId="gQC_geneSetModifyInput",
label = "Gene set to modify",
multiple = FALSE,
choices = c(defaultValue("gQC_geneSetModifyInput", "dummy")),
selected = defaultValue("gQC_geneSetModifyInput", "dummy"),
width = "100%",
options = list(maxItems = 1))
,
verbatimTextOutput("gQC_geneSetModifyInputGL") %>% jqui_resizable(),
sc_textInput(inputId= "gQC_geneSetModifynName", label="name of new gene set", value="newGeneSet"),
sc_textInput(inputId= "gQC_geneSetModifynDesc", label="description of new gene set", value="newGeneSet"),
sc_textInput(inputId= "gQC_geneSetModifyGenes", label="comma separated list of genes", value="") %>% jqui_resizable() ,
actionButton("geneSetModifyButton", "rename")
))
),
tabPanel(
title = "search gene sets", solidHeader = TRUE, width = 12, value = "gQC_search",
id = "gQC_search.Tab",
fluidRow(
column(
width = 6,
sc_textInput(inputId= "gQC_genesets_search", label="comma separated list of genes", value="") %>% jqui_resizable(),
#,
# actionButton("button_GSEA", "run GSEA")
),
column(width = 6,
sc_numericInput(inputId = "gQC_genesets_maxPrint", label="max items to print",
value=100, min=10, max=1000, step=10))),
fluidRow(
column(
width=12,
verbatimTextOutput("gQC_geneSetsearchOutput") %>% jqui_resizable()
)
)
)
)
)
# modTab ----
modTab <-
shinydashboard::tabItem(
"modifyProj",
fluidRow(div(h3("work with projections"), align = "center")),
br(),
tabBox(title = "modify projections", width = 12, id = "modProj",
tabPanel(
title = "Rename projections", solidHeader = TRUE, width = 12, value = "renameProj",
id = "rename.Proj.Tab",
fluidRow(
column(
width = 6,
sc_selectInput("oldPrj", "projections to copy + rename", choices = defaultValue("oldPrj", "notyet"), selected = defaultValue("oldPrj", "notyet"))
),
column(
width = 6,
fluidRow(
column(
width = 8,
sc_textInput("newPrj", "new name of Projection", value = defaultValue("newPrj", ""))
),
column(
width = 4,
actionButton("updatePrjsButton", "rename")
)
),
fluidRow(
column(
width = 8,
sc_selectInput("delPrj", "projections to delete", choices = defaultValue("delPrj", "notyet"), selected = defaultValue("delPrj", "notyet"))
),
column(
width = 4,
actionButton("delPrjsButton", "delete")
),
tags$style(type = "text/css", "#updatePrjsButton { width:100%; margin-top: 25px;}"),
tags$style(type = "text/css", "#delPrjsButton { width:100%; margin-top: 25px;}")
)
)
),
checkbsTT(item = "oldPrj"),
checkbsTT(item = "newPrj"),
checkbsTT(item = "updatePrjsButton"),
checkbsTT(item = "delPrj"),
checkbsTT(item = "delPrjsButton")
),
tabPanel(
title = "combine projections", solidHeader = TRUE, width = 12, value = "gQC_combProj",
id = "combine.Proj.Tab",
tags$p("Two factors can be combined by pasting the values per row and re-leveling"),
br(),
fluidRow(
column(
width = 6,
sc_selectInput("gQC_combPrj1", "1 st Projection", choices = c("notyet"), selected = "notyet")
),
column(
width = 6,
sc_selectInput("gQC_combPrj2", "2nd Projections", choices = c("notyet"), selected = "notyet")
)),
fluidRow(
column(width = 6,
sc_textInput("gQC_newCombPrj", "name of new Projection", value = "")),
column(
width = 6,
actionButton("gQC_updateCombPrjsButton", "apply")
)
),
fluidRow(column(
width = 12,
tableSelectionUi("gQC_projCombTableMod")
)
)
),
tabPanel(
title = "rename levels", width = 12, value = "gQC_renameLev",
id = "rename.Levels.Tab",
tags$p("rename the levels of a factor"),
br(),
fluidRow(
column(
width = 6,
sc_selectInput("gQC_rnProj", "Projection to modify", choices = c("notyet"), selected = "notyet")
),
column(width = 6,
sc_textInput("gQC_newRnPrj", "name of new Projection", value = ""))
),
fluidRow(
column(
width = 12,
tags$p(tags$b("original values")),
textOutput("gQC_orgLevels"),
br()
)
),
fluidRow(
column(
width = 12,
textAreaInput("gQC_renameLev", "new levels")
)
),
br(),
fluidRow(
column(
width = 6,
actionButton("gQC_renameLevButton", "apply")
)
)
),
tabPanel(
title = "rearrange levels", width = 12, value = "gQC_rearrangeLev",
id = "rearrange.Levels.Tab",
tags$p("rearrange the levels of a factor"),
br(),
fluidRow(
column(
width = 6,
sc_selectInput("gQC_raProj", "Projection to modify", choices = c("notyet"), selected = defaultValue("gQC_raProj", "notyet"))
),
column(width = 6,
sc_textInput("gQC_newRaPrj", "name of new Projection", value = ""))
),
fluidRow(
column(width = 12,
shinyjqui::orderInput('gQC_newRaLev', 'Rearrange levels', items = NULL, placeholder = 'choose projection...'),
)),
br(),
fluidRow(
column(
width = 6,
actionButton("gQC_rearrangeLevButton", "apply")
)
)
),
tabPanel(
title = "WIND", width = 12, value = "gQC_wind",
id = "wind.Tab",
tags$p("from WIND package compute hierachy of projection (https://github.com/haowulab/Wind)"),
tags$p("to compute weighted normalized mutual information (wNMI) and weighted Rand index (wRI) to evaluate the clustering results by comparing a clustering output with a reference which has a hierarchical structure."),
br(),
fluidRow(
column(
width = 6,
sc_selectInput("gQC_windProj", "Projection to use", choices = c("notyet"), selected = defaultValue("gQC_windProj", "notyet"))
)
),
fluidRow(
column(
width = 12,
plotOutput("gQC_windHC") %>% jqui_resizable()
)
)
)
)
)
tabList <- list(
shinydashboard::tabItem(
"gQC_umiHist",
tags$h3("Histogram of UMI counts"),
sc_numericInput("gQC_binSize", "number of bins", defaultValue("gQC_binSize",200), min=10),
fluidRow(column(
10,
offset = 0,
plotly::plotlyOutput("gQC_plotUmiHist") %>% jqui_resizable()
)),
br(),
actionButton("save2Histumi", "save to history")
),
shinydashboard::tabItem(
"gQC_sampleHist",
tags$h3("Histogram of cells per sample"),
fluidRow(column(
10,
offset = 0,
plotly::plotlyOutput("gQC_plotSampleHist") %>% jqui_resizable()
)),
br(),
actionButton("save2HistSample", "save to history")
),
shinydashboard::tabItem(
"gQC_variancePC",
tags$h3("Variance of PCs"),
fluidRow(column(
10,
offset = 0,
plotOutput("gQC_variancePCA") %>% jqui_resizable()
)),
br(),
actionButton("save2Histvar", "save to history")
),
shinydashboard::tabItem(
tabName = "gQC_tsnePlot",
# id = "gQC_tsneTab",
# shinyjs::useShinyjs(),
fluidRow(div(h3("tSNE Plot"), align = "center")),
br(),
shinydashboardPlus::box(
title = "tSNE parameters", solidHeader = TRUE, width = 12, status = "primary",
fluidRow(
column(
width = 6,
sc_numericInput("gQC_tsneDim", "Tsne dimensions", 3, min = 3, max = 3)
),
column(
width = 6,
sc_numericInput("gQC_tsnePerplexity", "Perplexity", defaultValue("gQC_tsnePerplexity", 10), min = 1, max = 100)
)
),
shinydashboardPlus::box(
title = "tSNE additional parameters", solidHeader = TRUE, width = 12, status = "primary",
id = "tSNEParametersToggle",
collapsible = TRUE, collapsed = TRUE,
column(
width = 6,
sc_numericInput("gQC_tsneTheta", "Theta", defaultValue("gQC_tsneTheta", 0.5), min = 0.0, max = 1, step = 0.1)
),
column(
width = 6,
sc_numericInput("gQC_tsneSeed", "Seed", defaultValue("gQC_tsneSeed", 1), min = 1, max = 10000)
)
),
checkbsTT(item = "gQC_tsneTheta"),
checkbsTT(item = "gQC_tsnePerplexity"),
fluidRow(
column(
width = 12, offset = 1,
# uiOutput("updatetsneParametersButton")
actionButton("updatetsneParameters", "apply changes", width = "80%")
# ,
# style = "color: #fff; background-color: #A00272; border-color: #2e6da4")
)
)
),
shinydashboardPlus::box(
title = "3D plot", solidHeader = TRUE, width = 12, status = "primary",
collapsible = TRUE, collapsed = FALSE, id = "tsne3D",
fluidRow(
column(
width = 3,
sc_selectInput("gQC_dim3D_x",
label = "X",
choices = c(defaultValue("gQC_dim3D_x", "tsne1"), "tsne2", "tsne3"),
selected = defaultValue("gQC_dim3D_x", "tsne1")
)
),
column(
width = 3,
sc_selectInput("gQC_dim3D_y",
label = "Y",
choices = c("tsne1", defaultValue("gQC_dim3D_y", "tsne2"), "tsne3"),
selected = defaultValue("gQC_dim3D_y", "tsne2")
)
),
column(
width = 3,
sc_selectInput("gQC_dim3D_z",
label = "Z",
choices = c("tsne1", "tsne2", defaultValue("gQC_dim3D_z", "tsne3")),
selected = defaultValue("gQC_dim3D_z", "tsne3")
)
),
column(
width = 3,
sc_selectInput("gQC_col3D",
label = "color",
choices = defaultValue("gQC_col3D", "sampleNames"),
selected = defaultValue("gQC_col3D", "sampleNames")
)
)
),
fluidRow(column(
width = 12,
plotly::plotlyOutput("gQC_tsne_main") %>% jqui_resizable()
))
),
checkbsTT("gQC_tsnePerplexity"),
checkbsTT("normalizationRadioButtonValue"),
checkbsTT("updateNormalization"),
br(),
shinydashboard::box(
title = "Table with all projections", solidHeader = TRUE, width = 12, status = "primary",
collapsible = FALSE, collapsed = FALSE,
fluidRow(column(
width = 12,
tableSelectionUi("gQC_projectionTableMod")
))
)
),
shinydashboard::tabItem(
tabName = "gQC_umapPlot",
shinydashboardPlus::box(
title = "UMAP parameters", solidHeader = TRUE, width = 12, status = "primary",
# id = "gQC_umapTab",
fluidRow(
column(
width = 12, offset = 1,
shinyWidgets::actionBttn("activateUMAP", "apply changes", style = "bordered")
)
),
br(),
fluidRow(
column(
width = 3,
sc_selectInput("gQC_um_n_neighbors",
label = "N Neighbors",
choices = c(2:100), selected = defaultValue("gQC_um_n_neighbors", "10")
)
),
column(
width = 3,
sc_selectInput("gQC_um_n_components",
label = "N components",
choices = c(2:20), selected = defaultValue("gQC_um_n_components", "3")
)
),
column(
width = 3,
sc_selectInput("gQC_um_spread",
label = "spread",
choices = c(1:10), selected = defaultValue("gQC_um_spread", "10")
)
),
column(
width = 3,
sc_selectInput("gQC_um_local_connectivity",
label = "local connectivity",
choices = 1:20, selected = defaultValue("gQC_um_local_connectivity", "5")
)
)
),
shinydashboardPlus::box(
title = "Addition UMAP options", solidHeader = TRUE, width = 12, status = "primary",
collapsible = TRUE, collapsed = TRUE,
id="addUMAPoptions",
fluidRow(
column(
width = 3,
sc_selectInput("gQC_um_randSeed",
label = "random seed",
choices = c(1:100), selected = defaultValue("gQC_um_randSeed", "1")
),
sc_selectInput("gQC_um_init",
label = "init",
choices = c("spectral", "random"), selected = defaultValue("gQC_um_init", "spectral")
)
),
column(
width = 3,
sc_selectInput(
"gQC_um_negative_sample_rate",
label = "negative sample rate",
choices = c(1:50), selected = defaultValue("gQC_um_negative_sample_rate", "5")
),
sc_selectInput("gQC_um_min_dist",
label = "min dist",
choices = seq(0.05, 0.5, 0.01), selected = defaultValue("gQC_um_min_dist", "0.01")
)
),
column(
width = 3,
sc_selectInput("gQC_um_metric",
label = "metric",
choices = c("euclidean", "manhattan", "cosine", "hamming"),
selected = defaultValue("gQC_um_metric", "euclidean")
),
sc_selectInput("gQC_um_set_op_mix_ratio",
label = "set op mix ratio",
choices = seq(0, 1, 0.1), selected = defaultValue("gQC_um_set_op_mix_ratio", "1")
)
),
column(
width = 3,
sc_numericInput(inputId = "gQC_um_n_epochs", label = "epochs:",
value = as.numeric(defaultValue("gQC_um_n_epochs", 200)), min = 1, max = 1000),
# selectizeInput("gQC_um_n_epochs",
# label = "epochs",
# choices = c(1:1000), selected = defaultValue("gQC_um_n_epochs", "200")
# ),
sc_selectInput(
"gQC_um_bandwidth",
label = "bandwidth",
choices = c(1:20), selected = defaultValue("gQC_um_bandwidth", "1")
),
checkbsTT("gQC_um_n_neighbors"),
checkbsTT("gQC_um_spread"),
checkbsTT("gQC_um_local_connectivity"),
checkbsTT("gQC_um_init"),
checkbsTT("gQC_um_negative_sample_rate"),
checkbsTT("gQC_um_min_dist"),
checkbsTT("gQC_um_metric"),
checkbsTT("gQC_um_set_op_mix_ratio"),
checkbsTT("gQC_um_bandwidth")
)
)
) # additional options box
),
shinydashboardPlus::box(
width = 12,
fluidRow(column(
width = 12,
clusterUI("gQC_umap_main")
))
)
),
modTab,
geneSetModTab,
if("DoubletFinder" %in% installed.packages()){
DoubletFinderTab
}
)
C3BI-pasteur-fr/UTechSCB-SCHNAPPs documentation built on Sept. 8, 2024, 12:44 a.m.
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# gQC_generalQC/ui.R
suppressMessages(require(magrittr))
source(paste0(packagePath, .Platform$file.sep , "modulesUI.R"), local = TRUE)
menuList <- list(
shinydashboard::menuItem("General QC",
# id="generalQCID",
tabName = "generalQC", icon = icon("thumbs-up"), startExpanded = FALSE,
shinydashboard::menuSubItem("UMI histogram", tabName = "gQC_umiHist"),
shinydashboard::menuSubItem("Sample histogram", tabName = "gQC_sampleHist"),
shinydashboard::menuSubItem("PC variance", tabName = "gQC_variancePC"),
if("DoubletFinder" %in% installed.packages()){
shinydashboard::menuSubItem("Doublet Finder", tabName = "gQC_doubletFinder")},
shinydashboard::menuSubItem("Scater QC", tabName = "DE_scaterQC")
# shinydashboard::menuSubItem("TSNE plot", tabName = "gQC_tsnePlot"),
# shinydashboard::menuSubItem("Umap", tabName = "gQC_umapPlot")
)
)
# gQC_doubletFinder ----
if("DoubletFinder" %in% installed.packages()){
DoubletFinderTab <- shinydashboard::tabItem(
tabName = "gQC_doubletFinder",
fluidRow(div(h3("DoubletFinder"), align = "center")),
br(),
tabBox(title = "", width = 12, id = "doubletFinderBox",
tabPanel(
title = "Doublet Finder", solidHeader = TRUE, width = 12, value = "doubletFinderTab",
id = "doublet.Finder.Tab",
fluidRow(
column(
width = 6,
sc_numericInput("GS_DF_dims", "PC imensions to use", min = 0, max = 200, step = 1, value = defaultValue("GS_DF_dims", 20))
),
column(
width = 6,
sc_numericInput("GS_DF_nRecover", "number of cells recovered by CellRanger (before QC)", min = 100, max = 20000000, step = 1000, value = defaultValue("GS_DF_nRecover", 10000))
)
),
fluidRow(
column(
width = 6,
sc_numericInput("GS_DF_pk", "neighborhood size to estimate likelihood of being doublet \n
(expressed as fraction of merged real-artifical data)", min = 0, max = Inf, step = 1, value = defaultValue("GS_DF_pk", 20))
),
column(
width = 6,
sc_numericInput("GS_DF_pN", "number of artificial doublets generated \n
(expressed as fraction of merged real-artifical data)", min = 0, max = 1, step = 0.01, value = defaultValue("GS_DF_pN", 0.10))
)
),
br(),
fluidRow(
column(
width = 12, offset = 1,
actionButton("GS_DF_button", "apply changes", width = "80%")
)
),
fluidRow(
column(
width = 12,
clusterUI("GS_DF_plot")
)
)
)
)
)
}
# geneSetModTab -----
geneSetModTab <- shinydashboard::tabItem(
tabName = "modifyGeneSets",
fluidRow(div(h3("work with gene sets"), align = "center")),
br(),
tabBox(title = "modify gene sets", width = 12, id = "modGS",
tabPanel(
title = "Rename gene set", solidHeader = TRUE, width = 12, value = "renameGS",
id = "rename.GS.Tab",
fluidRow(
column(
width = 6,
sc_selectInput("oldGS", "gene sets to copy + rename", choices = defaultValue("oldGS", "notyet"), selected = defaultValue("oldGS", "notyet")),
verbatimTextOutput("gQC_renameGenes") %>% jqui_resizable()
),
column(
width = 6,
fluidRow(
column(
width = 8,
sc_textInput("newGS", "new name of gene set", value = defaultValue("newGS", ""))
),
column(
width = 4,
actionButton("updateGSButton", "rename")
)
),
fluidRow(
column(
width = 8,
sc_selectInput("delGS", "gene set to delete", choices = defaultValue("delGS", "notyet"), selected = defaultValue("delGS", "notyet"))
),
column(
width = 4,
actionButton("delGSButton", "delete")
),
tags$style(type = "text/css", "#updateGSButton { width:100%; margin-top: 25px;}"),
tags$style(type = "text/css", "#delGSButton { width:100%; margin-top: 25px;}")
)
)
)
),
tabPanel(
title = "edit gene set", solidHeader = TRUE, width = 12, value = "gQC_editGS",
id = "gQC_editGS.Tab",
tags$p("Select a gene set and then edit it"),
fluidRow(
column(
width = 12,
sc_selectizeInput(inputId="gQC_geneSetModifyInput",
label = "Gene set to modify",
multiple = FALSE,
choices = c(defaultValue("gQC_geneSetModifyInput", "dummy")),
selected = defaultValue("gQC_geneSetModifyInput", "dummy"),
width = "100%",
options = list(maxItems = 1))
,
verbatimTextOutput("gQC_geneSetModifyInputGL") %>% jqui_resizable(),
sc_textInput(inputId= "gQC_geneSetModifynName", label="name of new gene set", value="newGeneSet"),
sc_textInput(inputId= "gQC_geneSetModifynDesc", label="description of new gene set", value="newGeneSet"),
sc_textInput(inputId= "gQC_geneSetModifyGenes", label="comma separated list of genes", value="") %>% jqui_resizable() ,
actionButton("geneSetModifyButton", "rename")
))
),
tabPanel(
title = "search gene sets", solidHeader = TRUE, width = 12, value = "gQC_search",
id = "gQC_search.Tab",
fluidRow(
column(
width = 6,
sc_textInput(inputId= "gQC_genesets_search", label="comma separated list of genes", value="") %>% jqui_resizable(),
#,
# actionButton("button_GSEA", "run GSEA")
),
column(width = 6,
sc_numericInput(inputId = "gQC_genesets_maxPrint", label="max items to print",
value=100, min=10, max=1000, step=10))),
fluidRow(
column(
width=12,
verbatimTextOutput("gQC_geneSetsearchOutput") %>% jqui_resizable()
)
)
)
)
)
# modTab ----
modTab <-
shinydashboard::tabItem(
"modifyProj",
fluidRow(div(h3("work with projections"), align = "center")),
br(),
tabBox(title = "modify projections", width = 12, id = "modProj",
tabPanel(
title = "Rename projections", solidHeader = TRUE, width = 12, value = "renameProj",
id = "rename.Proj.Tab",
fluidRow(
column(
width = 6,
sc_selectInput("oldPrj", "projections to copy + rename", choices = defaultValue("oldPrj", "notyet"), selected = defaultValue("oldPrj", "notyet"))
),
column(
width = 6,
fluidRow(
column(
width = 8,
sc_textInput("newPrj", "new name of Projection", value = defaultValue("newPrj", ""))
),
column(
width = 4,
actionButton("updatePrjsButton", "rename")
)
),
fluidRow(
column(
width = 8,
sc_selectInput("delPrj", "projections to delete", choices = defaultValue("delPrj", "notyet"), selected = defaultValue("delPrj", "notyet"))
),
column(
width = 4,
actionButton("delPrjsButton", "delete")
),
tags$style(type = "text/css", "#updatePrjsButton { width:100%; margin-top: 25px;}"),
tags$style(type = "text/css", "#delPrjsButton { width:100%; margin-top: 25px;}")
)
)
),
checkbsTT(item = "oldPrj"),
checkbsTT(item = "newPrj"),
checkbsTT(item = "updatePrjsButton"),
checkbsTT(item = "delPrj"),
checkbsTT(item = "delPrjsButton")
),
tabPanel(
title = "combine projections", solidHeader = TRUE, width = 12, value = "gQC_combProj",
id = "combine.Proj.Tab",
tags$p("Two factors can be combined by pasting the values per row and re-leveling"),
br(),
fluidRow(
column(
width = 6,
sc_selectInput("gQC_combPrj1", "1 st Projection", choices = c("notyet"), selected = "notyet")
),
column(
width = 6,
sc_selectInput("gQC_combPrj2", "2nd Projections", choices = c("notyet"), selected = "notyet")
)),
fluidRow(
column(width = 6,
sc_textInput("gQC_newCombPrj", "name of new Projection", value = "")),
column(
width = 6,
actionButton("gQC_updateCombPrjsButton", "apply")
)
),
fluidRow(column(
width = 12,
tableSelectionUi("gQC_projCombTableMod")
)
)
),
tabPanel(
title = "rename levels", width = 12, value = "gQC_renameLev",
id = "rename.Levels.Tab",
tags$p("rename the levels of a factor"),
br(),
fluidRow(
column(
width = 6,
sc_selectInput("gQC_rnProj", "Projection to modify", choices = c("notyet"), selected = "notyet")
),
column(width = 6,
sc_textInput("gQC_newRnPrj", "name of new Projection", value = ""))
),
fluidRow(
column(
width = 12,
tags$p(tags$b("original values")),
textOutput("gQC_orgLevels"),
br()
)
),
fluidRow(
column(
width = 12,
textAreaInput("gQC_renameLev", "new levels")
)
),
br(),
fluidRow(
column(
width = 6,
actionButton("gQC_renameLevButton", "apply")
)
)
),
tabPanel(
title = "rearrange levels", width = 12, value = "gQC_rearrangeLev",
id = "rearrange.Levels.Tab",
tags$p("rearrange the levels of a factor"),
br(),
fluidRow(
column(
width = 6,
sc_selectInput("gQC_raProj", "Projection to modify", choices = c("notyet"), selected = defaultValue("gQC_raProj", "notyet"))
),
column(width = 6,
sc_textInput("gQC_newRaPrj", "name of new Projection", value = ""))
),
fluidRow(
column(width = 12,
shinyjqui::orderInput('gQC_newRaLev', 'Rearrange levels', items = NULL, placeholder = 'choose projection...'),
)),
br(),
fluidRow(
column(
width = 6,
actionButton("gQC_rearrangeLevButton", "apply")
)
)
),
tabPanel(
title = "WIND", width = 12, value = "gQC_wind",
id = "wind.Tab",
tags$p("from WIND package compute hierachy of projection (https://github.com/haowulab/Wind)"),
tags$p("to compute weighted normalized mutual information (wNMI) and weighted Rand index (wRI) to evaluate the clustering results by comparing a clustering output with a reference which has a hierarchical structure."),
br(),
fluidRow(
column(
width = 6,
sc_selectInput("gQC_windProj", "Projection to use", choices = c("notyet"), selected = defaultValue("gQC_windProj", "notyet"))
)
),
fluidRow(
column(
width = 12,
plotOutput("gQC_windHC") %>% jqui_resizable()
)
)
)
)
)
tabList <- list(
shinydashboard::tabItem(
"gQC_umiHist",
tags$h3("Histogram of UMI counts"),
sc_numericInput("gQC_binSize", "number of bins", defaultValue("gQC_binSize",200), min=10),
fluidRow(column(
10,
offset = 0,
plotly::plotlyOutput("gQC_plotUmiHist") %>% jqui_resizable()
)),
br(),
actionButton("save2Histumi", "save to history")
),
shinydashboard::tabItem(
"gQC_sampleHist",
tags$h3("Histogram of cells per sample"),
fluidRow(column(
10,
offset = 0,
plotly::plotlyOutput("gQC_plotSampleHist") %>% jqui_resizable()
)),
br(),
actionButton("save2HistSample", "save to history")
),
shinydashboard::tabItem(
"gQC_variancePC",
tags$h3("Variance of PCs"),
fluidRow(column(
10,
offset = 0,
plotOutput("gQC_variancePCA") %>% jqui_resizable()
)),
br(),
actionButton("save2Histvar", "save to history")
),
shinydashboard::tabItem(
tabName = "gQC_tsnePlot",
# id = "gQC_tsneTab",
# shinyjs::useShinyjs(),
fluidRow(div(h3("tSNE Plot"), align = "center")),
br(),
shinydashboardPlus::box(
title = "tSNE parameters", solidHeader = TRUE, width = 12, status = "primary",
fluidRow(
column(
width = 6,
sc_numericInput("gQC_tsneDim", "Tsne dimensions", 3, min = 3, max = 3)
),
column(
width = 6,
sc_numericInput("gQC_tsnePerplexity", "Perplexity", defaultValue("gQC_tsnePerplexity", 10), min = 1, max = 100)
)
),
shinydashboardPlus::box(
title = "tSNE additional parameters", solidHeader = TRUE, width = 12, status = "primary",
id = "tSNEParametersToggle",
collapsible = TRUE, collapsed = TRUE,
column(
width = 6,
sc_numericInput("gQC_tsneTheta", "Theta", defaultValue("gQC_tsneTheta", 0.5), min = 0.0, max = 1, step = 0.1)
),
column(
width = 6,
sc_numericInput("gQC_tsneSeed", "Seed", defaultValue("gQC_tsneSeed", 1), min = 1, max = 10000)
)
),
checkbsTT(item = "gQC_tsneTheta"),
checkbsTT(item = "gQC_tsnePerplexity"),
fluidRow(
column(
width = 12, offset = 1,
# uiOutput("updatetsneParametersButton")
actionButton("updatetsneParameters", "apply changes", width = "80%")
# ,
# style = "color: #fff; background-color: #A00272; border-color: #2e6da4")
)
)
),
shinydashboardPlus::box(
title = "3D plot", solidHeader = TRUE, width = 12, status = "primary",
collapsible = TRUE, collapsed = FALSE, id = "tsne3D",
fluidRow(
column(
width = 3,
sc_selectInput("gQC_dim3D_x",
label = "X",
choices = c(defaultValue("gQC_dim3D_x", "tsne1"), "tsne2", "tsne3"),
selected = defaultValue("gQC_dim3D_x", "tsne1")
)
),
column(
width = 3,
sc_selectInput("gQC_dim3D_y",
label = "Y",
choices = c("tsne1", defaultValue("gQC_dim3D_y", "tsne2"), "tsne3"),
selected = defaultValue("gQC_dim3D_y", "tsne2")
)
),
column(
width = 3,
sc_selectInput("gQC_dim3D_z",
label = "Z",
choices = c("tsne1", "tsne2", defaultValue("gQC_dim3D_z", "tsne3")),
selected = defaultValue("gQC_dim3D_z", "tsne3")
)
),
column(
width = 3,
sc_selectInput("gQC_col3D",
label = "color",
choices = defaultValue("gQC_col3D", "sampleNames"),
selected = defaultValue("gQC_col3D", "sampleNames")
)
)
),
fluidRow(column(
width = 12,
plotly::plotlyOutput("gQC_tsne_main") %>% jqui_resizable()
))
),
checkbsTT("gQC_tsnePerplexity"),
checkbsTT("normalizationRadioButtonValue"),
checkbsTT("updateNormalization"),
br(),
shinydashboard::box(
title = "Table with all projections", solidHeader = TRUE, width = 12, status = "primary",
collapsible = FALSE, collapsed = FALSE,
fluidRow(column(
width = 12,
tableSelectionUi("gQC_projectionTableMod")
))
)
),
shinydashboard::tabItem(
tabName = "gQC_umapPlot",
shinydashboardPlus::box(
title = "UMAP parameters", solidHeader = TRUE, width = 12, status = "primary",
# id = "gQC_umapTab",
fluidRow(
column(
width = 12, offset = 1,
shinyWidgets::actionBttn("activateUMAP", "apply changes", style = "bordered")
)
),
br(),
fluidRow(
column(
width = 3,
sc_selectInput("gQC_um_n_neighbors",
label = "N Neighbors",
choices = c(2:100), selected = defaultValue("gQC_um_n_neighbors", "10")
)
),
column(
width = 3,
sc_selectInput("gQC_um_n_components",
label = "N components",
choices = c(2:20), selected = defaultValue("gQC_um_n_components", "3")
)
),
column(
width = 3,
sc_selectInput("gQC_um_spread",
label = "spread",
choices = c(1:10), selected = defaultValue("gQC_um_spread", "10")
)
),
column(
width = 3,
sc_selectInput("gQC_um_local_connectivity",
label = "local connectivity",
choices = 1:20, selected = defaultValue("gQC_um_local_connectivity", "5")
)
)
),
shinydashboardPlus::box(
title = "Addition UMAP options", solidHeader = TRUE, width = 12, status = "primary",
collapsible = TRUE, collapsed = TRUE,
id="addUMAPoptions",
fluidRow(
column(
width = 3,
sc_selectInput("gQC_um_randSeed",
label = "random seed",
choices = c(1:100), selected = defaultValue("gQC_um_randSeed", "1")
),
sc_selectInput("gQC_um_init",
label = "init",
choices = c("spectral", "random"), selected = defaultValue("gQC_um_init", "spectral")
)
),
column(
width = 3,
sc_selectInput(
"gQC_um_negative_sample_rate",
label = "negative sample rate",
choices = c(1:50), selected = defaultValue("gQC_um_negative_sample_rate", "5")
),
sc_selectInput("gQC_um_min_dist",
label = "min dist",
choices = seq(0.05, 0.5, 0.01), selected = defaultValue("gQC_um_min_dist", "0.01")
)
),
column(
width = 3,
sc_selectInput("gQC_um_metric",
label = "metric",
choices = c("euclidean", "manhattan", "cosine", "hamming"),
selected = defaultValue("gQC_um_metric", "euclidean")
),
sc_selectInput("gQC_um_set_op_mix_ratio",
label = "set op mix ratio",
choices = seq(0, 1, 0.1), selected = defaultValue("gQC_um_set_op_mix_ratio", "1")
)
),
column(
width = 3,
sc_numericInput(inputId = "gQC_um_n_epochs", label = "epochs:",
value = as.numeric(defaultValue("gQC_um_n_epochs", 200)), min = 1, max = 1000),
# selectizeInput("gQC_um_n_epochs",
# label = "epochs",
# choices = c(1:1000), selected = defaultValue("gQC_um_n_epochs", "200")
# ),
sc_selectInput(
"gQC_um_bandwidth",
label = "bandwidth",
choices = c(1:20), selected = defaultValue("gQC_um_bandwidth", "1")
),
checkbsTT("gQC_um_n_neighbors"),
checkbsTT("gQC_um_spread"),
checkbsTT("gQC_um_local_connectivity"),
checkbsTT("gQC_um_init"),
checkbsTT("gQC_um_negative_sample_rate"),
checkbsTT("gQC_um_min_dist"),
checkbsTT("gQC_um_metric"),
checkbsTT("gQC_um_set_op_mix_ratio"),
checkbsTT("gQC_um_bandwidth")
)
)
) # additional options box
),
shinydashboardPlus::box(
width = 12,
fluidRow(column(
width = 12,
clusterUI("gQC_umap_main")
))
)
),
modTab,
geneSetModTab,
if("DoubletFinder" %in% installed.packages()){
DoubletFinderTab
}
)
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