inst/app/app.R
In eisascience/HISTA: The Human Infertility Single-cell Testis Atlas Shiny App. Jan.26.2021
# Human Infertility Single-cell Testis Atlas (HISTA)
# HISTA -----
## libraries -----
library(shiny)
library(rclipboard)
library(shinydashboard)
library(ggplot2)
library(data.table)
library(ggrepel)
library(viridis)
library(ggnewscale)
library(RColorBrewer)
library(grid)
library(gridExtra)
require(dplyr)
library(ggrastr)
library(ggpubr)
library(DT)
library(knitr)
# library(HISTA)
## Inputs -----
pathi = getwd()
source("app_Fxs.R",local = TRUE)
# source(paste0(pathi, "inst/app/app_Fxs.R"))
# list2env(readRDS( paste0(pathi, "/data/HISTAv1_dataLS_feb2022.rds")), envir = globalenv()) #for deploy on shinyapps
#monkey shiny server do has SCRATCH_DIR defined
if (Sys.getenv("SCRATCH_DIR") != "") {
pathi = paste0(Sys.getenv("SCRATCH_DIR"), "/data")
load.data.path = paste0(pathi, "/ConradLab/HISTA/HISTAv1_dataLS_June2023.rds" )
} else {
load.data.path = paste0(pathi, "/HISTAv1_dataLS_June2023.rds" )
if(!file.exists(load.data.path)) {
load.data.path = paste0(pathi, "/data/HISTAv1_dataLS_June2023.rds" )
}
}
list2env(readRDS(load.data.path), envir = globalenv())
## Palettes -----
# palettes <- ggthemes::ggthemes_data[["tableau"]][["color-palettes"]][["regular"]]$`Tableau 20`$value
col_vector = c("#7FC97F", "#38170B", "#BEAED4", "#BF1B0B", "#FFC465", "#386CB0",
"#66ADE5", "#F0027F", "#252A52", "#BF5B17", "#999999", "#666666",
"#E69F00", "#1B9E77", "#7570B3", "#F0E442", "#B07AA1", "#F28E2B",
"#FFBE7D", "#59A14F", "#8CD17D", "#B6992D", "#F1CE63", "#499894",
"#86BCB6", "#E15759", "#FF9D9A", "#79706E", "#BAB0AC", "#D37295",
"#FABFD2", "#E7298A", "#D4A6C8", "#9D7660", "#D7B5A6","#e6194b",
"#666666", "#3cb44b", "#A6CEE3", "#ffe119", "#1F78B4", "#B15928")
# UI -----
ui <- dashboardPage(
dashboardHeader(title = "HISTA v2.9.7"
),
## Dashboard -----
dashboardSidebar(
sidebarMenu(
menuItem("Home Page", tabName = "homepage", icon = icon("home"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Main tab", tabName = "maintab", icon = icon("star"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Index of Components", tabName = "sdaindex", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Fingerprinting (heatmap)", tabName = "chisqrSDAenrichHeatmaps", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Gene Expr per cond (boxplot)", tabName = "geneExprPerCond", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Gene Expr per cell type (boxplot)", tabName = "geneExprPerCT", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Gene Expr per cell type (2D)", tabName = "geneExprPerCT2D", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Cell score per cell type (boxplot)", tabName = "SDAscorePerCT", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Cell score per cell type (2D)", tabName = "DimReduxCT2D", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Metadata per cell type (2D)", tabName = "DimReduxCT_meta2D", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Gene Correlations", tabName = "GeneCor", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Component Corrrelations", tabName = "CompCor", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
#menuItem("Score order per. Comp", tabName = "CellScoreOrderingSDA", icon = icon("plus"),
#badgeLabel = "final", badgeColor = "green"),
menuItem("Pseudotime Meta (germ only)", tabName = "pseudotimeSDA", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Pseudotime Gene (germ only)", tabName = "pseudotimeSDAgene", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Pseudotime Component Index", tabName = "pseudotimeSDAIndex", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Enrichment Analysis", tabName = "Enrichment", icon = icon("plus"),#asterisk
badgeLabel = "final", badgeColor = "green"),
menuItem("Top Loaded Components", tabName = "TopLoadedComps", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("lncRNAs", tabName = "lncRNA_expr_toploaded", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("DE genes", tabName = "DEgenes", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Soma only W. LN19", tabName = "somaWLN", icon = icon("asterisk"), #minus
badgeLabel = "final", badgeColor = "green"),
menuItem("LC only W. Zhao21", tabName = "LConly", icon = icon("asterisk"),
badgeLabel = "final", badgeColor = "green"),
menuItem("User Manual", tabName = "usermanual", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Version History", tabName = "versionhistory", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Cite Me", tabName = "citation", icon = icon("book"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Conrad Lab", icon = icon("book"),
href = "https://conradlab.org"),
menuItem("@eisamahyari", icon = icon("heart"),
href = "https://eisascience.github.io")
)
),
## Dash Body -----
dashboardBody(
### Tab Items -----
tabItems(
#### template tabs
# tabItem(tabName = "germdash",
# h2("Germ only"),
# fluidRow(
#
# )
# ),
### homepage -----
tabItem(tabName = "homepage",
h2("Welcome to HISTA's Homepage"),
fluidRow(
imageOutput("homepage", width = 900)
)
),
### main tab -----
# First
tabItem(tabName = "maintab",
fluidRow(
box(
title = "Inputs", status = "warning", solidHeader = TRUE,
#"Box content here", br(), "More box content",
#sliderInput("ComponentN", "Slider input:", 1, 150, 1),
textInput("ComponentNtext", "SDA component search (numerical):", "1"),
textInput("Genetext", "Gene search (text input):", "PRM1"),
radioButtons("data", "Data origin:",
c("tSNE - Batch-removed SDA-CellScores" = "tsneBrSDACS",
"UMAP - Batch-removed SDA-CellScores" = "umapBrSDACS",
"tSNE - DropSim Norm. DGE" = "tsneDSNDGE",
#"Batch-removed-Imputed-DGE" = "DGEimp",
#"DromSim-Normalized-DGE" = "DGEnorm",
#"tSNE - Seurat-Norm. DGE" = "tsneSNDGE",
"tSNE - Batch-removed-Imputed-DGE" = "tsneImpDGE"
)),
radioButtons("metaselect", "Metadata Selection:",
c("Cell types" = "celltype",
"Donor-replicates" = "donrep",
"Donors" = "donor",
"Condition" = "COND.ID",
"Experiments" = "experiment",
"CellCycle" = "Phase"
)),
textInput("NoOfGenes", "No. of Genes to output:", "20"),
actionButton("C2Cpos", "Copy2ClipPosGenes (local only)"),
actionButton("C2Cneg", "Copy2ClipNegGenes (local only)"),
downloadButton("TXTall", "Copy2TxtAll (any browser"),
actionButton("PrevSDA", "Prev SDA"),
actionButton("NextSDA", "Next SDA"),
#actionButton("ScreenShot", "Take a screenshot"),
width = 3
),
valueBoxOutput("CellType1", width = 3),
valueBoxOutput("GeneName", width = 3)
),
box(
title = "Gene expr", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
downloadButton("tSNEwGeneExpr_download"),
plotOutput("tSNE_geneExpr"), #plotlyOutput
width = 5
),
box(
#actionButton("button", "Next"),
title = "Cell score", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
downloadButton("tSNEwSDAScoreProj_download"),
plotOutput("tSNEwSDAScoreProj"), #plotlyOutput
width = 5
),
box(
title = "Pheno - tSNE", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
downloadButton("tSNEwMeta_download"),
plotOutput("tSNEwMeta"), #plotlyOutput
width = 5
),
box(
title = "Pheno Legend", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
plotOutput("tSNEwMetaLegend"),
width = 5
),
box(
downloadButton("SDAScoresAcross_download"),
title = "Cell Scores Across", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
plotOutput("SDAScoresAcross", height = 400),
width = 10
),
box(
title = "Pos. Loadings GO", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
downloadButton("SDAGOpos_download"),
plotOutput("GOpos"), #plotlyOutput
width = 5
),
box(
title = "Neg. Loadings GO", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
downloadButton("SDAGOneg_download"),
plotOutput("GOneg"),
width = 5
),
box(
title = "Chrom. Location", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
downloadButton("ChrLoc_download"),
plotOutput("ChrLoc"),
width = 10
),
box(title = "Pos. Top Genes", status = "info", solidHeader = TRUE, width = 4,
tableOutput("packageTablePos")
),
box(title = "Neg. Top Genes", status = "info", solidHeader = TRUE, width = 4,
tableOutput("packageTableNeg")
)
),
### sdaindex -----
tabItem(tabName = "sdaindex",
h2("Index of SDA components and annotation"),
fluidRow(
DT::dataTableOutput("SDAannotations")
)
),
### versionhistory -----
tabItem(tabName = "versionhistory",
h2("Version History"),
fluidRow(
uiOutput('VerHistHTML')
)
),
### usermanual -----
tabItem(tabName = "usermanual",
h2("User Manual"),
fluidRow(
uiOutput('UserManualHTML')
)
),
### pseudotimeSDAIndex -----
tabItem(tabName = "pseudotimeSDAIndex",
h2("Index of SDA components and their pseudo-order"),
fluidRow(
DT::dataTableOutput("SDApseudotime")
)
),
### DEgenes -----
tabItem(tabName = "DEgenes",
h2("Cell Types and Transcriptional Groups"),
fluidRow(
box(
title = "DE Genes", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
selectInput("DEgenes_selectedItem", "Select an item:", choices = names(DEgenes)[1:4]),
selectInput("DEgenes_selectedDEDF", "Select an item:", ""),
width = 5, background = "black"
),
box(
title = "DE Genes", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
DTOutput("DEgenes_dataTable"),
width = 20
)
)
),
### ChisqrHeatmaps -----
tabItem(tabName = "chisqrSDAenrichHeatmaps",
h2("SDA component pathology fingerprinting"),
fluidRow(
box(title = "ChiSqrRes Scores Pos cellscores", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
radioButtons("clustStat_chisqr", "Hierarchical cluster:",
c("Cluster" = "True",
"No Cluster" = "False"
)),
radioButtons("metaselect_chisqr", "Metadata Selection:",
c("Cell types" = "celltype",
"Donor-replicates" = "donrep",
"Donors" = "donor",
"Condition" = "COND.ID",
"Experiments" = "experiment",
"CellCycle" = "Phase"
), selected = "experiment"),
width = 5#, background = "black"
),
box(
title = "ChiSqrRes Scores Pos cellscores", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
downloadButton("SDAScoresChiPos_download"),
plotOutput("SDAScoresChiPos", height = 400),
width = 10, background = "black"
),
box(
title = "ChiSqrRes Scores Neg cellscores", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
downloadButton("SDAScoresChiNeg_download"),
plotOutput("SDAScoresChiNeg", height = 400),
width = 10, background = "black"
),
)
),
### geneExprPerCT2D -----
tabItem(tabName = "geneExprPerCT2D",
h2("Gene expr by cell type"),
fluidRow(
box(
title = "Inputs 2", status = "warning", solidHeader = TRUE,
#"Box content here", br(), "More box content",
#sliderInput("ComponentN", "Slider input:", 1, 150, 1),
width = 5,
textInput("Genetext_celltype_gex", "Gene search (text input):", "PRM1"),
radioButtons("DimReduxCT_ctselect_gex", "Celltype Selection:",
c("Leydig" = "leydig",
"Sertoli" = "sertoli",
"Myoid" = "myoid",
"Neuro" = "neuro",
"Germ-All" = "germ",
"Germ-UndiffSg" = "germ_UnDiffSgSct",
"Germ-DiffSg" = "germ_DiffSgSct",
"Germ-PrePachSct" = "germ_PrePachSct",
"Germ-PachSct" = "germ_PachSct",
"Germ_Std" = "germ_Std",
"Endothelial" = "endothelial",
"Myeloid" = "myeloid",
"Adaptive" = "adaptive",
"All" = "all"
), selected = "all")
),
box(title = "DimRedux", status = "warning", solidHeader = TRUE,
radioButtons("data2", "Data origin:",
c("tSNE - Batch-removed SDA-CellScores" = "tsneBrSDACS",
"UMAP - Batch-removed SDA-CellScores" = "umapBrSDACS",
"tSNE - DropSim Norm. DGE" = "tsneDSNDGE",
#"Batch-removed-Imputed-DGE" = "DGEimp",
#"DromSim-Normalized-DGE" = "DGEnorm",
#"tSNE - Seurat-Norm. DGE" = "tsneSNDGE",
"tSNE - Batch-removed-Imputed-DGE" = "tsneImpDGE"
)),
width = 5
),
box(
title = "Gene expr Projected per CellType", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
downloadButton("DimReduxCT_gex_download"),
plotOutput("DimReduxCT_GEX"),
width = 10
)
)
),
### DimReduxCT2D -----
tabItem(tabName = "DimReduxCT2D",
h2("SDA score by cell type"),
fluidRow(
box(title = "DimRedux", status = "warning", solidHeader = TRUE,
radioButtons("data3", "Data origin:",
c("tSNE - Batch-removed SDA-CellScores" = "tsneBrSDACS",
"UMAP - Batch-removed SDA-CellScores" = "umapBrSDACS",
"tSNE - DropSim Norm. DGE" = "tsneDSNDGE",
#"Batch-removed-Imputed-DGE" = "DGEimp",
#"DromSim-Normalized-DGE" = "DGEnorm",
#"tSNE - Seurat-Norm. DGE" = "tsneSNDGE",
"tSNE - Batch-removed-Imputed-DGE" = "tsneImpDGE"
)),
width = 5
),
box(
title = "Inputs 2", status = "warning", solidHeader = TRUE,
#"Box content here", br(), "More box content",
#sliderInput("ComponentN", "Slider input:", 1, 150, 1),
width = 5,
textInput("ComponentNtext_DimReduxCT", "SDA component search (numerical):", "1"),
radioButtons("DimReduxCT_ctselect", "Celltype Selection:",
c("Leydig" = "leydig",
"Sertoli" = "sertoli",
"Myoid" = "myoid",
"Neuro" = "neuro",
"Germ-All" = "germ",
"Germ-UndiffSg" = "germ_UnDiffSgSct",
"Germ-DiffSg" = "germ_DiffSgSct",
"Germ-PrePachSct" = "germ_PrePachSct",
"Germ-PachSct" = "germ_PachSct",
"Germ_Std" = "germ_Std",
"Endothelial" = "endothelial",
"Myeloid" = "myeloid",
"Adaptive" = "adaptive",
"All" = "all"
), selected = "all")
),
box(
title = "SDA score Projected per CellType", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
downloadButton("DimReduxCT_download"),
plotOutput("DimReduxCT2D"),
width = 10
)
)
),
### DimReduxCT_meta2D -----
tabItem(tabName = "DimReduxCT_meta2D",
h2("Metadata by cell type"),
fluidRow(
box(title = "DimRedux", status = "warning", solidHeader = TRUE,
radioButtons("data4", "Data origin:",
c("tSNE - Batch-removed SDA-CellScores" = "tsneBrSDACS",
"UMAP - Batch-removed SDA-CellScores" = "umapBrSDACS",
"tSNE - DropSim Norm. DGE" = "tsneDSNDGE",
#"Batch-removed-Imputed-DGE" = "DGEimp",
#"DromSim-Normalized-DGE" = "DGEnorm",
#"tSNE - Seurat-Norm. DGE" = "tsneSNDGE",
"tSNE - Batch-removed-Imputed-DGE" = "tsneImpDGE"
)),
width = 5
),
box(
title = "Inputs 2", status = "warning", solidHeader = TRUE,
#"Box content here", br(), "More box content",
#sliderInput("ComponentN", "Slider input:", 1, 150, 1),
width = 5,
radioButtons("DimReduxCT_ctselect_meta", "Celltype Selection:",
c("Leydig" = "leydig",
"Sertoli" = "sertoli",
"Myoid" = "myoid",
"Neuro" = "neuro",
"Germ-All" = "germ",
"Germ-UndiffSg" = "germ_UnDiffSgSct",
"Germ-DiffSg" = "germ_DiffSgSct",
"Germ-PrePachSct" = "germ_PrePachSct",
"Germ-PachSct" = "germ_PachSct",
"Germ_Std" = "germ_Std",
"Endothelial" = "endothelial",
"Myeloid" = "myeloid",
"Adaptive" = "adaptive",
"All" = "all"
), selected = "all"),
radioButtons("ctselect_meta", "Metadata Selection:",
c("Cell types" = "celltype",
"Donor-replicates" = "donrep",
"Donors" = "donor",
"Condition" = "COND.ID",
"Experiments" = "experiment",
"CellCycle" = "Phase"
)),
),
box(
title = "SDA score Projected per CellType", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
downloadButton("DimReduxCT_meta2D_download"),
plotOutput("DimReduxCT_meta2D"),
width = 10
)
)
),
### geneExprPerCond -----
tabItem(tabName = "geneExprPerCond",
h2("Gene Expression Stat. Sig."),
fluidRow(
box(
title = "Inputs", status = "warning", solidHeader = TRUE,
#"Box content here", br(), "More box content",
#sliderInput("ComponentN", "Slider input:", 1, 150, 1),
width = 5,
textInput("Genetext2", "Text input:", "STAR"),
radioButtons("metaselect2", "Metadata Selection:",
c("Experiments" = "experiment"
))
),
box(
title = "Inputs 2", status = "warning", solidHeader = TRUE,
#"Box content here", br(), "More box content",
#sliderInput("ComponentN", "Slider input:", 1, 150, 1),
width = 5,
radioButtons("celltypeselect2", "Celltype Selection:",
c("Leydig" = "leydig",
"Sertoli" = "sertoli",
"Myoid" = "myoid",
"Neuro" = "neuro",
"Germ-All" = "germ",
"Germ-UndiffSg" = "germ_UnDiffSgSct",
"Germ-DiffSg" = "germ_DiffSgSct",
"Germ-PrePachSct" = "germ_PrePachSct",
"Germ-PachSct" = "germ_PachSct",
"Germ_Std" = "germ_Std",
"Endothelial" = "endothelial",
"Myeloid" = "myeloid",
"Adaptive" = "adaptive",
"All" = "all"
))
),
box(
title = "Gene Expression Stat. Sig. Meta", status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
downloadButton("geneExprPerCond_download"),
plotOutput("geneExprPerCond_box"),
width = 10
)
)
),
### geneExprPerCT -----
tabItem(tabName = "geneExprPerCT",
h2("Gene Expression per Cell Types"),
fluidRow(
box(
title = "Inputs", status = "warning", solidHeader = TRUE,
#"Box content here", br(), "More box content",
#sliderInput("ComponentN", "Slider input:", 1, 150, 1),
width = 5,
textInput("Genetext3", "Text input:", "STAR"),
radioButtons("metaselect3", "Phenotype scope:",
c("Pheno" = "scope1"
)),
radioButtons("condSelect1", "Conditions:",
c("All donors" = "all",
"Adult controls" = "cnt",
"Inf 1" = "inf1",
"Inf 2" = "inf2",
"KS" = "ks",
"JUV"= "juv"
), selected = "cnt")
),
box(
title = "Gene Expression Stat. Sig. Meta", status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
downloadButton("geneExprPerCT_download"),
plotOutput("geneExprPerCT_box"),
width = 10
)
)
),
### SDAscorePerCT -----
tabItem(tabName = "SDAscorePerCT",
h2("SDA score per Cell types"),
fluidRow(
box(
title = "Inputs", status = "warning", solidHeader = TRUE,
width = 5,
textInput("celltypes_sdaN_in", "SDA component search (numerical):", "1")),
box(title = "Conditions", status = "warning", solidHeader = TRUE,
width = 5,
radioButtons("celltypes_condSelect", "Conditions:",
c("All donors" = "all",
"Adult controls" = "cnt",
"Inf 1" = "inf1",
"Inf 2" = "inf2",
"KS" = "ks",
"JUV"= "juv"
), selected = "cnt"
),
),
box(title = "SDA score per cell type", status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
downloadButton("celltypes_SDAperCT_box_download"),
plotOutput("celltypes_SDAperCT_box",
height = 400),
width = 10
)
)
),
### Cell score ordering -----
tabItem(tabName = "CellScoreOrderingSDA",
h2("Cell Score Ordering"),
fluidRow(
box(
title = "Inputs", status = "warning", solidHeader = TRUE,
#"Box content here", br(), "More box content",
#sliderInput("ComponentN", "Slider input:", 1, 150, 1),
textInput("ComponentNtext2", "SDA component search (numerical):", "1"),
# radioButtons("metaselect3", "Metadata Selection:",
# c("Experiments" = "experiment"
# )),
radioButtons("celltypeselect3", "Celltype Selection:",
c("Leydig" = "leydig",
"Sertoli" = "sertoli",
"Myoid" = "myoid",
"Neuro" = "neuro",
"Germ-All" = "germ",
"Germ-UndiffSg" = "germ_UnDiffSgSct",
"Germ-DiffSg" = "germ_DiffSgSct",
"Germ-PrePachSct" = "germ_PrePachSct",
"Germ-PachSct" = "germ_PachSct",
"Germ_Std" = "germ_Std",
"Endothelial" = "endothelial",
"Myeloid" = "myeloid",
"Adaptive" = "adaptive",
"All" = "all"
))
),
box(title = "SDA comp scores ordered", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
plotOutput("CellScoreOrderSDA", height = 800),
width = 10
)
)
),
### Pseudotime -----
tabItem(tabName = "pseudotimeSDA",
h2("Pseudotime of Germ Cells Only"),
fluidRow(
box(title = "Inputs", status = "warning", solidHeader = TRUE,
textInput("ComponentName_pseudo", "SDA component search (numerical):", "1"),
radioButtons("metaselect_pseudo", "Metadata Selection:",
c("Pseudotime" = "pseudotime",
"Cell types" = "celltype",
"Donor-replicates" = "donrep",
"Donors" = "donor",
"Condition" = "COND.ID",
"Experiments" = "experiment",
"CellCycle" = "Phase"
)),
width = 3),
box(title = "Germ Cell Only tSNE", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
plotOutput("tSNEPseudoSDA", height = 400),
),
box(title = "Pseudotime", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
downloadButton("PseudotimeSDA_download"),
plotOutput("PseudotimeSDA", height = 400),
width = 10
)
)
),
### Pseudotime gene -----
tabItem(tabName = "pseudotimeSDAgene",
h2("Gene expr on Pseudotime of Germ Cells Only"),
fluidRow(
box(title = "Inputs", status = "warning", solidHeader = TRUE,
textInput("Genetext_pseudo", "Gene search (text input):", "PRM1"),
radioButtons("metaselect_pseudo_gene", "Metadata Selection:",
c("Cell types" = "celltype",
"Donor-replicates" = "donrep",
"Donors" = "donor",
"Condition" = "COND.ID",
"Experiments" = "experiment",
"CellCycle" = "Phase"
), selected = "Phase"),
width = 5
),
box(title = "Gene Expr Pseudotime", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
downloadButton("PseudotimeSDA_gene_download"),
plotOutput("PseudotimeSDAgene", height = 400),
plotOutput("PseudotimeSDAgeneMeta", height = 400),
width = 10
)
)
),
### Enrichment -----
tabItem(tabName = "Enrichment",
fluidRow(
box(
title = "Inputs", status = "warning", solidHeader = TRUE,
"Multiple formatting of gene sets accepted",
br(), "List can be seperated by comma e.g. from ",
br(), " or spaces e.g. from Excel",
br(), "Also, single or double quotes or not",
#sliderInput("ComponentN", "Slider input:", 1, 150, 1),
textInput("GeneSet", "A set of genes", "'PRM1', 'SPATA42', 'SPRR4', 'NUPR2', 'HBZ', 'DYNLL2'"),
width = 8
),
box(
title = "Positive Loadings", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
plotOutput("PosEnrichPlot"),
width = 10
),
box(
title = "Negative Loadings", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
plotOutput("NegEnrichPlot"),
width = 10
)
)
),
### TopLoadedComps -----
tabItem(tabName = "TopLoadedComps",
fluidRow(
box(
title = "Inputs", status = "warning", solidHeader = TRUE,
"Multiple formatting of gene sets accepted",
br(), "List can be seperated by comma e.g. from ",
br(), " or spaces e.g. from Excel",
br(), "Also, single or double quotes or not",
br(), "This works best with larger sets of genes!",
br(), "As an example set, here are all the -AS genes",
#sliderInput("ComponentN", "Slider input:", 1, 150, 1),
textInput("GeneSet_TLC", "A set of genes", "'AADACL2-AS1', 'C21orf62-AS1', 'DLGAP2-AS1', 'TRIM31-AS1', 'MAMDC2-AS1', 'KCNQ1-AS1',
'MIF-AS1', 'KANSL1-AS1', 'MAPT-AS1', 'LENG8-AS1', 'DDX39B-AS1', 'FAM181A-AS1', 'ITPK1-AS1',
'SERTAD4-AS1', 'ZFY-AS1', 'GLIS2-AS1', 'ZNF436-AS1', 'EPHA1-AS1', 'MCPH1-AS1', 'SLC14A2-AS1',
'DHRS4-AS1', 'PPP4R1-AS1', 'C1RL-AS1', 'AQP4-AS1', 'MCM8-AS1', 'SIRPG-AS1', 'TTC39C-AS1',
'ISM1-AS1', 'MACROD2-AS1', 'TTC3-AS1', 'ASMTL-AS1', 'CACNA1C-AS4', 'CACNA1C-AS2',
'KCNK15-AS1', 'USP12-AS2', 'ARHGAP5-AS1', 'STK4-AS1', 'PAN3-AS1', 'HORMAD2-AS1',
'TEX26-AS1', 'SLC25A21-AS1', 'DLGAP1-AS3', 'URB1-AS1', 'ZNF295-AS1', 'ZNF674-AS1',
'ITCH-AS1', 'EP300-AS1', 'FUT8-AS1', 'USP12-AS1', 'DIAPH3-AS1', 'MIS18A-AS1', 'PCDH9-AS4',
'NDFIP2-AS1', 'BRWD1-AS2', 'BRWD1-AS1', 'BMP7-AS1', 'STX18-AS1', 'PRR34-AS1', 'RBM26-AS1',
'FGF13-AS1', 'WASF3-AS1', 'DSG2-AS1', 'FOXN3-AS1', 'PCDH9-AS3', 'RAP2C-AS1', 'UCKL1-AS1',
'B4GALT1-AS1', 'TAPT1-AS1', 'ZNF337-AS1', 'CTBP1-AS', 'DIO2-AS1', 'TRPM2-AS', 'TSPEAR-AS1',
'TSPEAR-AS2', 'FRMD6-AS1', 'ST8SIA6-AS1', 'EFCAB6-AS1', 'FRMD6-AS2', 'PCCA-AS1', 'CDKN2B-AS1',
'SCEL-AS1', 'MCM3AP-AS1', 'ADORA2A-AS1', 'GPC5-AS2', 'LY86-AS1', 'PCDH9-AS1', 'PROSER2-AS1',
'TSC22D1-AS1', 'SGMS1-AS1', 'FAM83C-AS1', 'MORC2-AS1', 'PARD3-AS1', 'F10-AS1', 'JARID2-AS1',
'LNX1-AS1', 'FAM170B-AS1', 'ELOVL2-AS1', 'IGF2-AS', 'MGAT3-AS1', 'UBOX5-AS1', 'PAXBP1-AS1',
'ITGB2-AS1', 'HM13-AS1', 'ZNF503-AS2', 'GRID1-AS1', 'JMJD1C-AS1', 'PRMT5-AS1', 'KIZ-AS1',
'EDNRB-AS1', 'MACC1-AS1', 'ZNF341-AS1', 'NAV2-AS5', 'GPC6-AS1', 'FGF14-AS1', 'MORF4L2-AS1',
'SYP-AS1', 'FGF14-AS2', 'BDNF-AS', 'PLCG1-AS1', 'A2ML1-AS1', 'GABRG3-AS1', 'BTBD9-AS1',
'TRAM2-AS1', 'PPP1R26-AS1', 'SACS-AS1', 'RNASEH2B-AS1', 'PLBD1-AS1', 'SLC39A12-AS1', 'COL5A1-AS1',
'CSE1L-AS1', 'DSG1-AS1', 'OGFR-AS1', 'VPS13A-AS1', 'PRRX2-AS1', 'FAM53B-AS1', 'MCHR2-AS1', 'SNCA-AS1',
'WDFY3-AS1', 'NRSN2-AS1', 'DBH-AS1', 'IQCH-AS1', 'ARNTL2-AS1', 'THAP9-AS1', 'ADNP-AS1', 'SLC25A25-AS1',
'LZTS1-AS1', 'ZNRF3-AS1', 'ODF2-AS1', 'GAS6-AS1', 'HOXC-AS1', 'TEX36-AS1', 'FOCAD-AS1', 'RARA-AS1',
'LMO7-AS1', 'EDRF1-AS1', 'ZBTB46-AS1', 'TPT1-AS1', 'USP2-AS1', 'SLC25A30-AS1', 'GSN-AS1', 'IFT74-AS1',
'HTR2A-AS1', 'DIAPH3-AS2', 'ARAP1-AS2'"),
width = 5
)),
box(
title = "Top positive loaded comps", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
plotOutput("TopLoadComp_Plot"),
width = 5
),
box(
title = "Enrichment across components", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
plotOutput("TopLoadedBarplot"),
width = 10
),
box(
title = "Cor(loadings) of SDA components", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
downloadButton("CompCorCustPlot_download"),
plotOutput("CompCorCustPlot"),
width = 10
)
),
### lncRNA_expr_toploaded -----
tabItem(tabName = "lncRNA_expr_toploaded",
fluidRow(
box(
title = "Selection of component", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
textInput("ComponentNtext_lncRNATopLoaded", "SDA component search (numerical):", "1"),
# plotOutput("lncRNA_topLoaded"),
width = 5
),
box(
title = "Top Loaded lncRNAs Neg and Pos", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
textOutput("lncRNAgenes_Neg_txt"),
textOutput("lncRNAgenes_Pos_txt"),
width = 10
),
box(
title = "Overlap of lncRNAs (biomaRt 04/2022)", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
plotOutput("lncRNA_Venn"),
width = 5
),
box(
title = "Distribution of lncRNAs vs Random gene set", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
plotOutput("lncRNA_toploaded"),
width = 5
),
box(
title = "Enrichment across components", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
plotOutput("lncRNA_BarplotSDA"),
width = 10
)
# valueBoxOutput("lncRNAgenes", width = NULL),
)
),
### CompCor -----
tabItem(tabName = "CompCor",
fluidRow(
valueBoxOutput("CorPlot_CellType1", width = 3),
box(
title = "Cor(loadings) of SDA components", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
textInput("CompCorSDAnum", "Top 150 genes of SDA component (numerical):", "1"),
sliderInput(inputId = "CompCorSDAnum_ngene",
label = "Number of top genes:",
min = 10,
max = 150,
value = 24),
downloadButton("CompCorPlot_download"),
plotOutput("CompCorPlot"),
width = 10
),
box(
title = "Top Loaded genes", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
textOutput("top_Neg_txt"),
textOutput("top_Peg_txt"),
width = 10
)
)
),
### CompCor -----
tabItem(tabName = "GeneCor",
fluidRow(
# valueBoxOutput("CorPlot_CellType1", width = 3),
box(
radioButtons("celltypeselect_geneCor", "Celltype Selection:",
c("Leydig" = "leydig",
"Sertoli" = "sertoli",
"Myoid" = "myoid",
"Neuro" = "neuro",
"Germ-All" = "germ",
"Germ-UndiffSg" = "germ_UnDiffSgSct",
"Germ-DiffSg" = "germ_DiffSgSct",
"Germ-PrePachSct" = "germ_PrePachSct",
"Germ-PachSct" = "germ_PachSct",
"Germ_Std" = "germ_Std",
"Endothelial" = "endothelial",
"Myeloid" = "myeloid",
"Adaptive" = "adaptive",
"All" = "all"
), selected = "germ_UnDiffSgSct"),
width = 5
),
box(
title = "Cor(GEX) gene expression correlation", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
textInput("GeneSet_geneCor", "A set of genes", "'NANOS1', 'NANOS2', 'NANOS3', 'DMRT1', 'KIT', 'PLPPR3', 'CCK', 'HES5', 'PLPPR5', 'RHCE', 'SCT', 'FAM25G', 'DPPA4', 'TDRD1', 'MAGEA4', 'STRA8', 'DPPA4', 'TDRD1', 'MAGEA4', 'STRA8', 'GFRA1', 'BCL6B', 'ID4', 'PIWIL4', 'DNMT1', 'DMRT1', 'KIT', 'DMC1', 'SYCP3', 'ETV5', 'EGR4'"),
downloadButton("GeneCorPlot_download"),
plotOutput("GeneCorPlot"),
width = 10
)
)
),
## External Data -----
### Soma only w LN19 -----
tabItem(tabName = "somaWLN",
h2("Reprocessing of: \nMahyari-Conrad et al. (2021) + \n Laurentino-Neuhaus (2019)*"),
fluidRow(
box(
title = "Phenotype", status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
downloadButton("tsnesomaonlywln_phenotype_download"),
plotOutput("tSNE_somaWLN_Pheno3_Rx"),
width = 5,
# footer = "* Laurentino et al. 2019 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6714305/"
),
box(
title = "Condition", status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
downloadButton("tsnesomaonlywln_condition_download"),
plotOutput("tSNE_somaWLN_COND.ID_Rx"),
width = 5,
# footer = "* Laurentino et al. 2019 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6714305/"
),
box(
title = "Donors", status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
downloadButton("tsnesomaonlywln_donor_download"),
plotOutput("tSNE_somaWLN_DONR.ID_Rx"),
width = 5,
footer = "* Laurentino et al. 2019 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6714305/"
),
box(
title = "Total No. of transcripts", status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
downloadButton("tsnesomaonlywln_ncount_download"),
plotOutput("tSNE_somaWLN_nCount_RNA_Rx"),
width = 5,
# footer = "* Laurentino et al. 2019 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6714305/"
)
)
),
### LC only w Zhao20 LN19 -----
tabItem(tabName = "LConly",
h2("Reprocessing of Leydig Cells (LC): \nMahyari-Conrad et al. (2021) + \n Laurentino-Neuhaus (2019) + \n Zhao-Li (2020)**"),
fluidRow(
box(
title = "Mahyari et al. only data", status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
# downloadButton("tsnesomaonlywln_donor_download"),
plotOutput("DimRedux_LConly_donors_Rx"),
width = 5,
#footer = "* Laurentino et al. 2019 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6714305/ \n** Zhao et al. 2020 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7655944/"
),
box(
title = "Mahyari et al. only data", status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
# downloadButton("tsnesomaonlywln_donor_download"),
plotOutput("DimRedux_LConly_phenotype_Rx"),
width = 5,
#footer = "* Laurentino et al. 2019 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6714305/ \n** Zhao et al. 2020 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7655944/"
),
box(
title = "LC from Mahyari21 + LN19 + Zhao20", status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
# downloadButton("tsnesomaonlywln_donor_download"),
plotOutput("DimRedux_LConlyZhao_donors_Rx"),
width = 5,
footer = "* Laurentino et al. 2019 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6714305/ \n** Zhao et al. 2020 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7655944/"
),
box(
title = "LC from Mahyari21 + LN19 + Zhao20", status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
# downloadButton("tsnesomaonlywln_donor_download"),
plotOutput("DimRedux_LConlyZhao_phenotype_Rx"),
width = 5,
#footer = "* Laurentino et al. 2019 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6714305/ \n** Zhao et al. 2020 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7655944/"
),
box(
title = "LC from Mahyari21 + LN19 + Zhao20", status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
# downloadButton("tsnesomaonlywln_donor_download"),
plotOutput("DimRedux_LConlyZhao_phenotypeProp_Rx"),
width = 5,
#footer = "* Laurentino et al. 2019 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6714305/ \n** Zhao et al. 2020 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7655944/"
),
box(
title = "LC from Mahyari21 + LN19 + Zhao20", status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
# downloadButton("tsnesomaonlywln_donor_download"),
plotOutput("DimRedux_LConlyZhao_KeyGenesViolin_Rx"),
width = 10,
#footer = "* Laurentino et al. 2019 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6714305/ \n** Zhao et al. 2020 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7655944/"
),
)
)
)#tabitems
)#dashboardBody
)#dashboardPage
# Server -----
server <- function(input, output, session) {
source("app_server.R",local = TRUE)
}
shinyApp(ui, server)
eisascience/HISTA documentation built on Jan. 28, 2024, 4:06 a.m.
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# Human Infertility Single-cell Testis Atlas (HISTA)
# HISTA -----
## libraries -----
library(shiny)
library(rclipboard)
library(shinydashboard)
library(ggplot2)
library(data.table)
library(ggrepel)
library(viridis)
library(ggnewscale)
library(RColorBrewer)
library(grid)
library(gridExtra)
require(dplyr)
library(ggrastr)
library(ggpubr)
library(DT)
library(knitr)
# library(HISTA)
## Inputs -----
pathi = getwd()
source("app_Fxs.R",local = TRUE)
# source(paste0(pathi, "inst/app/app_Fxs.R"))
# list2env(readRDS( paste0(pathi, "/data/HISTAv1_dataLS_feb2022.rds")), envir = globalenv()) #for deploy on shinyapps
#monkey shiny server do has SCRATCH_DIR defined
if (Sys.getenv("SCRATCH_DIR") != "") {
pathi = paste0(Sys.getenv("SCRATCH_DIR"), "/data")
load.data.path = paste0(pathi, "/ConradLab/HISTA/HISTAv1_dataLS_June2023.rds" )
} else {
load.data.path = paste0(pathi, "/HISTAv1_dataLS_June2023.rds" )
if(!file.exists(load.data.path)) {
load.data.path = paste0(pathi, "/data/HISTAv1_dataLS_June2023.rds" )
}
}
list2env(readRDS(load.data.path), envir = globalenv())
## Palettes -----
# palettes <- ggthemes::ggthemes_data[["tableau"]][["color-palettes"]][["regular"]]$`Tableau 20`$value
col_vector = c("#7FC97F", "#38170B", "#BEAED4", "#BF1B0B", "#FFC465", "#386CB0",
"#66ADE5", "#F0027F", "#252A52", "#BF5B17", "#999999", "#666666",
"#E69F00", "#1B9E77", "#7570B3", "#F0E442", "#B07AA1", "#F28E2B",
"#FFBE7D", "#59A14F", "#8CD17D", "#B6992D", "#F1CE63", "#499894",
"#86BCB6", "#E15759", "#FF9D9A", "#79706E", "#BAB0AC", "#D37295",
"#FABFD2", "#E7298A", "#D4A6C8", "#9D7660", "#D7B5A6","#e6194b",
"#666666", "#3cb44b", "#A6CEE3", "#ffe119", "#1F78B4", "#B15928")
# UI -----
ui <- dashboardPage(
dashboardHeader(title = "HISTA v2.9.7"
),
## Dashboard -----
dashboardSidebar(
sidebarMenu(
menuItem("Home Page", tabName = "homepage", icon = icon("home"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Main tab", tabName = "maintab", icon = icon("star"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Index of Components", tabName = "sdaindex", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Fingerprinting (heatmap)", tabName = "chisqrSDAenrichHeatmaps", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Gene Expr per cond (boxplot)", tabName = "geneExprPerCond", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Gene Expr per cell type (boxplot)", tabName = "geneExprPerCT", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Gene Expr per cell type (2D)", tabName = "geneExprPerCT2D", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Cell score per cell type (boxplot)", tabName = "SDAscorePerCT", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Cell score per cell type (2D)", tabName = "DimReduxCT2D", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Metadata per cell type (2D)", tabName = "DimReduxCT_meta2D", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Gene Correlations", tabName = "GeneCor", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Component Corrrelations", tabName = "CompCor", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
#menuItem("Score order per. Comp", tabName = "CellScoreOrderingSDA", icon = icon("plus"),
#badgeLabel = "final", badgeColor = "green"),
menuItem("Pseudotime Meta (germ only)", tabName = "pseudotimeSDA", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Pseudotime Gene (germ only)", tabName = "pseudotimeSDAgene", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Pseudotime Component Index", tabName = "pseudotimeSDAIndex", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Enrichment Analysis", tabName = "Enrichment", icon = icon("plus"),#asterisk
badgeLabel = "final", badgeColor = "green"),
menuItem("Top Loaded Components", tabName = "TopLoadedComps", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("lncRNAs", tabName = "lncRNA_expr_toploaded", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("DE genes", tabName = "DEgenes", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Soma only W. LN19", tabName = "somaWLN", icon = icon("asterisk"), #minus
badgeLabel = "final", badgeColor = "green"),
menuItem("LC only W. Zhao21", tabName = "LConly", icon = icon("asterisk"),
badgeLabel = "final", badgeColor = "green"),
menuItem("User Manual", tabName = "usermanual", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Version History", tabName = "versionhistory", icon = icon("plus"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Cite Me", tabName = "citation", icon = icon("book"),
badgeLabel = "final", badgeColor = "green"),
menuItem("Conrad Lab", icon = icon("book"),
href = "https://conradlab.org"),
menuItem("@eisamahyari", icon = icon("heart"),
href = "https://eisascience.github.io")
)
),
## Dash Body -----
dashboardBody(
### Tab Items -----
tabItems(
#### template tabs
# tabItem(tabName = "germdash",
# h2("Germ only"),
# fluidRow(
#
# )
# ),
### homepage -----
tabItem(tabName = "homepage",
h2("Welcome to HISTA's Homepage"),
fluidRow(
imageOutput("homepage", width = 900)
)
),
### main tab -----
# First
tabItem(tabName = "maintab",
fluidRow(
box(
title = "Inputs", status = "warning", solidHeader = TRUE,
#"Box content here", br(), "More box content",
#sliderInput("ComponentN", "Slider input:", 1, 150, 1),
textInput("ComponentNtext", "SDA component search (numerical):", "1"),
textInput("Genetext", "Gene search (text input):", "PRM1"),
radioButtons("data", "Data origin:",
c("tSNE - Batch-removed SDA-CellScores" = "tsneBrSDACS",
"UMAP - Batch-removed SDA-CellScores" = "umapBrSDACS",
"tSNE - DropSim Norm. DGE" = "tsneDSNDGE",
#"Batch-removed-Imputed-DGE" = "DGEimp",
#"DromSim-Normalized-DGE" = "DGEnorm",
#"tSNE - Seurat-Norm. DGE" = "tsneSNDGE",
"tSNE - Batch-removed-Imputed-DGE" = "tsneImpDGE"
)),
radioButtons("metaselect", "Metadata Selection:",
c("Cell types" = "celltype",
"Donor-replicates" = "donrep",
"Donors" = "donor",
"Condition" = "COND.ID",
"Experiments" = "experiment",
"CellCycle" = "Phase"
)),
textInput("NoOfGenes", "No. of Genes to output:", "20"),
actionButton("C2Cpos", "Copy2ClipPosGenes (local only)"),
actionButton("C2Cneg", "Copy2ClipNegGenes (local only)"),
downloadButton("TXTall", "Copy2TxtAll (any browser"),
actionButton("PrevSDA", "Prev SDA"),
actionButton("NextSDA", "Next SDA"),
#actionButton("ScreenShot", "Take a screenshot"),
width = 3
),
valueBoxOutput("CellType1", width = 3),
valueBoxOutput("GeneName", width = 3)
),
box(
title = "Gene expr", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
downloadButton("tSNEwGeneExpr_download"),
plotOutput("tSNE_geneExpr"), #plotlyOutput
width = 5
),
box(
#actionButton("button", "Next"),
title = "Cell score", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
downloadButton("tSNEwSDAScoreProj_download"),
plotOutput("tSNEwSDAScoreProj"), #plotlyOutput
width = 5
),
box(
title = "Pheno - tSNE", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
downloadButton("tSNEwMeta_download"),
plotOutput("tSNEwMeta"), #plotlyOutput
width = 5
),
box(
title = "Pheno Legend", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
plotOutput("tSNEwMetaLegend"),
width = 5
),
box(
downloadButton("SDAScoresAcross_download"),
title = "Cell Scores Across", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
plotOutput("SDAScoresAcross", height = 400),
width = 10
),
box(
title = "Pos. Loadings GO", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
downloadButton("SDAGOpos_download"),
plotOutput("GOpos"), #plotlyOutput
width = 5
),
box(
title = "Neg. Loadings GO", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
downloadButton("SDAGOneg_download"),
plotOutput("GOneg"),
width = 5
),
box(
title = "Chrom. Location", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
downloadButton("ChrLoc_download"),
plotOutput("ChrLoc"),
width = 10
),
box(title = "Pos. Top Genes", status = "info", solidHeader = TRUE, width = 4,
tableOutput("packageTablePos")
),
box(title = "Neg. Top Genes", status = "info", solidHeader = TRUE, width = 4,
tableOutput("packageTableNeg")
)
),
### sdaindex -----
tabItem(tabName = "sdaindex",
h2("Index of SDA components and annotation"),
fluidRow(
DT::dataTableOutput("SDAannotations")
)
),
### versionhistory -----
tabItem(tabName = "versionhistory",
h2("Version History"),
fluidRow(
uiOutput('VerHistHTML')
)
),
### usermanual -----
tabItem(tabName = "usermanual",
h2("User Manual"),
fluidRow(
uiOutput('UserManualHTML')
)
),
### pseudotimeSDAIndex -----
tabItem(tabName = "pseudotimeSDAIndex",
h2("Index of SDA components and their pseudo-order"),
fluidRow(
DT::dataTableOutput("SDApseudotime")
)
),
### DEgenes -----
tabItem(tabName = "DEgenes",
h2("Cell Types and Transcriptional Groups"),
fluidRow(
box(
title = "DE Genes", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
selectInput("DEgenes_selectedItem", "Select an item:", choices = names(DEgenes)[1:4]),
selectInput("DEgenes_selectedDEDF", "Select an item:", ""),
width = 5, background = "black"
),
box(
title = "DE Genes", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
DTOutput("DEgenes_dataTable"),
width = 20
)
)
),
### ChisqrHeatmaps -----
tabItem(tabName = "chisqrSDAenrichHeatmaps",
h2("SDA component pathology fingerprinting"),
fluidRow(
box(title = "ChiSqrRes Scores Pos cellscores", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
radioButtons("clustStat_chisqr", "Hierarchical cluster:",
c("Cluster" = "True",
"No Cluster" = "False"
)),
radioButtons("metaselect_chisqr", "Metadata Selection:",
c("Cell types" = "celltype",
"Donor-replicates" = "donrep",
"Donors" = "donor",
"Condition" = "COND.ID",
"Experiments" = "experiment",
"CellCycle" = "Phase"
), selected = "experiment"),
width = 5#, background = "black"
),
box(
title = "ChiSqrRes Scores Pos cellscores", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
downloadButton("SDAScoresChiPos_download"),
plotOutput("SDAScoresChiPos", height = 400),
width = 10, background = "black"
),
box(
title = "ChiSqrRes Scores Neg cellscores", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
downloadButton("SDAScoresChiNeg_download"),
plotOutput("SDAScoresChiNeg", height = 400),
width = 10, background = "black"
),
)
),
### geneExprPerCT2D -----
tabItem(tabName = "geneExprPerCT2D",
h2("Gene expr by cell type"),
fluidRow(
box(
title = "Inputs 2", status = "warning", solidHeader = TRUE,
#"Box content here", br(), "More box content",
#sliderInput("ComponentN", "Slider input:", 1, 150, 1),
width = 5,
textInput("Genetext_celltype_gex", "Gene search (text input):", "PRM1"),
radioButtons("DimReduxCT_ctselect_gex", "Celltype Selection:",
c("Leydig" = "leydig",
"Sertoli" = "sertoli",
"Myoid" = "myoid",
"Neuro" = "neuro",
"Germ-All" = "germ",
"Germ-UndiffSg" = "germ_UnDiffSgSct",
"Germ-DiffSg" = "germ_DiffSgSct",
"Germ-PrePachSct" = "germ_PrePachSct",
"Germ-PachSct" = "germ_PachSct",
"Germ_Std" = "germ_Std",
"Endothelial" = "endothelial",
"Myeloid" = "myeloid",
"Adaptive" = "adaptive",
"All" = "all"
), selected = "all")
),
box(title = "DimRedux", status = "warning", solidHeader = TRUE,
radioButtons("data2", "Data origin:",
c("tSNE - Batch-removed SDA-CellScores" = "tsneBrSDACS",
"UMAP - Batch-removed SDA-CellScores" = "umapBrSDACS",
"tSNE - DropSim Norm. DGE" = "tsneDSNDGE",
#"Batch-removed-Imputed-DGE" = "DGEimp",
#"DromSim-Normalized-DGE" = "DGEnorm",
#"tSNE - Seurat-Norm. DGE" = "tsneSNDGE",
"tSNE - Batch-removed-Imputed-DGE" = "tsneImpDGE"
)),
width = 5
),
box(
title = "Gene expr Projected per CellType", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
downloadButton("DimReduxCT_gex_download"),
plotOutput("DimReduxCT_GEX"),
width = 10
)
)
),
### DimReduxCT2D -----
tabItem(tabName = "DimReduxCT2D",
h2("SDA score by cell type"),
fluidRow(
box(title = "DimRedux", status = "warning", solidHeader = TRUE,
radioButtons("data3", "Data origin:",
c("tSNE - Batch-removed SDA-CellScores" = "tsneBrSDACS",
"UMAP - Batch-removed SDA-CellScores" = "umapBrSDACS",
"tSNE - DropSim Norm. DGE" = "tsneDSNDGE",
#"Batch-removed-Imputed-DGE" = "DGEimp",
#"DromSim-Normalized-DGE" = "DGEnorm",
#"tSNE - Seurat-Norm. DGE" = "tsneSNDGE",
"tSNE - Batch-removed-Imputed-DGE" = "tsneImpDGE"
)),
width = 5
),
box(
title = "Inputs 2", status = "warning", solidHeader = TRUE,
#"Box content here", br(), "More box content",
#sliderInput("ComponentN", "Slider input:", 1, 150, 1),
width = 5,
textInput("ComponentNtext_DimReduxCT", "SDA component search (numerical):", "1"),
radioButtons("DimReduxCT_ctselect", "Celltype Selection:",
c("Leydig" = "leydig",
"Sertoli" = "sertoli",
"Myoid" = "myoid",
"Neuro" = "neuro",
"Germ-All" = "germ",
"Germ-UndiffSg" = "germ_UnDiffSgSct",
"Germ-DiffSg" = "germ_DiffSgSct",
"Germ-PrePachSct" = "germ_PrePachSct",
"Germ-PachSct" = "germ_PachSct",
"Germ_Std" = "germ_Std",
"Endothelial" = "endothelial",
"Myeloid" = "myeloid",
"Adaptive" = "adaptive",
"All" = "all"
), selected = "all")
),
box(
title = "SDA score Projected per CellType", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
downloadButton("DimReduxCT_download"),
plotOutput("DimReduxCT2D"),
width = 10
)
)
),
### DimReduxCT_meta2D -----
tabItem(tabName = "DimReduxCT_meta2D",
h2("Metadata by cell type"),
fluidRow(
box(title = "DimRedux", status = "warning", solidHeader = TRUE,
radioButtons("data4", "Data origin:",
c("tSNE - Batch-removed SDA-CellScores" = "tsneBrSDACS",
"UMAP - Batch-removed SDA-CellScores" = "umapBrSDACS",
"tSNE - DropSim Norm. DGE" = "tsneDSNDGE",
#"Batch-removed-Imputed-DGE" = "DGEimp",
#"DromSim-Normalized-DGE" = "DGEnorm",
#"tSNE - Seurat-Norm. DGE" = "tsneSNDGE",
"tSNE - Batch-removed-Imputed-DGE" = "tsneImpDGE"
)),
width = 5
),
box(
title = "Inputs 2", status = "warning", solidHeader = TRUE,
#"Box content here", br(), "More box content",
#sliderInput("ComponentN", "Slider input:", 1, 150, 1),
width = 5,
radioButtons("DimReduxCT_ctselect_meta", "Celltype Selection:",
c("Leydig" = "leydig",
"Sertoli" = "sertoli",
"Myoid" = "myoid",
"Neuro" = "neuro",
"Germ-All" = "germ",
"Germ-UndiffSg" = "germ_UnDiffSgSct",
"Germ-DiffSg" = "germ_DiffSgSct",
"Germ-PrePachSct" = "germ_PrePachSct",
"Germ-PachSct" = "germ_PachSct",
"Germ_Std" = "germ_Std",
"Endothelial" = "endothelial",
"Myeloid" = "myeloid",
"Adaptive" = "adaptive",
"All" = "all"
), selected = "all"),
radioButtons("ctselect_meta", "Metadata Selection:",
c("Cell types" = "celltype",
"Donor-replicates" = "donrep",
"Donors" = "donor",
"Condition" = "COND.ID",
"Experiments" = "experiment",
"CellCycle" = "Phase"
)),
),
box(
title = "SDA score Projected per CellType", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
downloadButton("DimReduxCT_meta2D_download"),
plotOutput("DimReduxCT_meta2D"),
width = 10
)
)
),
### geneExprPerCond -----
tabItem(tabName = "geneExprPerCond",
h2("Gene Expression Stat. Sig."),
fluidRow(
box(
title = "Inputs", status = "warning", solidHeader = TRUE,
#"Box content here", br(), "More box content",
#sliderInput("ComponentN", "Slider input:", 1, 150, 1),
width = 5,
textInput("Genetext2", "Text input:", "STAR"),
radioButtons("metaselect2", "Metadata Selection:",
c("Experiments" = "experiment"
))
),
box(
title = "Inputs 2", status = "warning", solidHeader = TRUE,
#"Box content here", br(), "More box content",
#sliderInput("ComponentN", "Slider input:", 1, 150, 1),
width = 5,
radioButtons("celltypeselect2", "Celltype Selection:",
c("Leydig" = "leydig",
"Sertoli" = "sertoli",
"Myoid" = "myoid",
"Neuro" = "neuro",
"Germ-All" = "germ",
"Germ-UndiffSg" = "germ_UnDiffSgSct",
"Germ-DiffSg" = "germ_DiffSgSct",
"Germ-PrePachSct" = "germ_PrePachSct",
"Germ-PachSct" = "germ_PachSct",
"Germ_Std" = "germ_Std",
"Endothelial" = "endothelial",
"Myeloid" = "myeloid",
"Adaptive" = "adaptive",
"All" = "all"
))
),
box(
title = "Gene Expression Stat. Sig. Meta", status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
downloadButton("geneExprPerCond_download"),
plotOutput("geneExprPerCond_box"),
width = 10
)
)
),
### geneExprPerCT -----
tabItem(tabName = "geneExprPerCT",
h2("Gene Expression per Cell Types"),
fluidRow(
box(
title = "Inputs", status = "warning", solidHeader = TRUE,
#"Box content here", br(), "More box content",
#sliderInput("ComponentN", "Slider input:", 1, 150, 1),
width = 5,
textInput("Genetext3", "Text input:", "STAR"),
radioButtons("metaselect3", "Phenotype scope:",
c("Pheno" = "scope1"
)),
radioButtons("condSelect1", "Conditions:",
c("All donors" = "all",
"Adult controls" = "cnt",
"Inf 1" = "inf1",
"Inf 2" = "inf2",
"KS" = "ks",
"JUV"= "juv"
), selected = "cnt")
),
box(
title = "Gene Expression Stat. Sig. Meta", status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
downloadButton("geneExprPerCT_download"),
plotOutput("geneExprPerCT_box"),
width = 10
)
)
),
### SDAscorePerCT -----
tabItem(tabName = "SDAscorePerCT",
h2("SDA score per Cell types"),
fluidRow(
box(
title = "Inputs", status = "warning", solidHeader = TRUE,
width = 5,
textInput("celltypes_sdaN_in", "SDA component search (numerical):", "1")),
box(title = "Conditions", status = "warning", solidHeader = TRUE,
width = 5,
radioButtons("celltypes_condSelect", "Conditions:",
c("All donors" = "all",
"Adult controls" = "cnt",
"Inf 1" = "inf1",
"Inf 2" = "inf2",
"KS" = "ks",
"JUV"= "juv"
), selected = "cnt"
),
),
box(title = "SDA score per cell type", status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
downloadButton("celltypes_SDAperCT_box_download"),
plotOutput("celltypes_SDAperCT_box",
height = 400),
width = 10
)
)
),
### Cell score ordering -----
tabItem(tabName = "CellScoreOrderingSDA",
h2("Cell Score Ordering"),
fluidRow(
box(
title = "Inputs", status = "warning", solidHeader = TRUE,
#"Box content here", br(), "More box content",
#sliderInput("ComponentN", "Slider input:", 1, 150, 1),
textInput("ComponentNtext2", "SDA component search (numerical):", "1"),
# radioButtons("metaselect3", "Metadata Selection:",
# c("Experiments" = "experiment"
# )),
radioButtons("celltypeselect3", "Celltype Selection:",
c("Leydig" = "leydig",
"Sertoli" = "sertoli",
"Myoid" = "myoid",
"Neuro" = "neuro",
"Germ-All" = "germ",
"Germ-UndiffSg" = "germ_UnDiffSgSct",
"Germ-DiffSg" = "germ_DiffSgSct",
"Germ-PrePachSct" = "germ_PrePachSct",
"Germ-PachSct" = "germ_PachSct",
"Germ_Std" = "germ_Std",
"Endothelial" = "endothelial",
"Myeloid" = "myeloid",
"Adaptive" = "adaptive",
"All" = "all"
))
),
box(title = "SDA comp scores ordered", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
plotOutput("CellScoreOrderSDA", height = 800),
width = 10
)
)
),
### Pseudotime -----
tabItem(tabName = "pseudotimeSDA",
h2("Pseudotime of Germ Cells Only"),
fluidRow(
box(title = "Inputs", status = "warning", solidHeader = TRUE,
textInput("ComponentName_pseudo", "SDA component search (numerical):", "1"),
radioButtons("metaselect_pseudo", "Metadata Selection:",
c("Pseudotime" = "pseudotime",
"Cell types" = "celltype",
"Donor-replicates" = "donrep",
"Donors" = "donor",
"Condition" = "COND.ID",
"Experiments" = "experiment",
"CellCycle" = "Phase"
)),
width = 3),
box(title = "Germ Cell Only tSNE", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
plotOutput("tSNEPseudoSDA", height = 400),
),
box(title = "Pseudotime", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
downloadButton("PseudotimeSDA_download"),
plotOutput("PseudotimeSDA", height = 400),
width = 10
)
)
),
### Pseudotime gene -----
tabItem(tabName = "pseudotimeSDAgene",
h2("Gene expr on Pseudotime of Germ Cells Only"),
fluidRow(
box(title = "Inputs", status = "warning", solidHeader = TRUE,
textInput("Genetext_pseudo", "Gene search (text input):", "PRM1"),
radioButtons("metaselect_pseudo_gene", "Metadata Selection:",
c("Cell types" = "celltype",
"Donor-replicates" = "donrep",
"Donors" = "donor",
"Condition" = "COND.ID",
"Experiments" = "experiment",
"CellCycle" = "Phase"
), selected = "Phase"),
width = 5
),
box(title = "Gene Expr Pseudotime", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
downloadButton("PseudotimeSDA_gene_download"),
plotOutput("PseudotimeSDAgene", height = 400),
plotOutput("PseudotimeSDAgeneMeta", height = 400),
width = 10
)
)
),
### Enrichment -----
tabItem(tabName = "Enrichment",
fluidRow(
box(
title = "Inputs", status = "warning", solidHeader = TRUE,
"Multiple formatting of gene sets accepted",
br(), "List can be seperated by comma e.g. from ",
br(), " or spaces e.g. from Excel",
br(), "Also, single or double quotes or not",
#sliderInput("ComponentN", "Slider input:", 1, 150, 1),
textInput("GeneSet", "A set of genes", "'PRM1', 'SPATA42', 'SPRR4', 'NUPR2', 'HBZ', 'DYNLL2'"),
width = 8
),
box(
title = "Positive Loadings", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
plotOutput("PosEnrichPlot"),
width = 10
),
box(
title = "Negative Loadings", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
plotOutput("NegEnrichPlot"),
width = 10
)
)
),
### TopLoadedComps -----
tabItem(tabName = "TopLoadedComps",
fluidRow(
box(
title = "Inputs", status = "warning", solidHeader = TRUE,
"Multiple formatting of gene sets accepted",
br(), "List can be seperated by comma e.g. from ",
br(), " or spaces e.g. from Excel",
br(), "Also, single or double quotes or not",
br(), "This works best with larger sets of genes!",
br(), "As an example set, here are all the -AS genes",
#sliderInput("ComponentN", "Slider input:", 1, 150, 1),
textInput("GeneSet_TLC", "A set of genes", "'AADACL2-AS1', 'C21orf62-AS1', 'DLGAP2-AS1', 'TRIM31-AS1', 'MAMDC2-AS1', 'KCNQ1-AS1',
'MIF-AS1', 'KANSL1-AS1', 'MAPT-AS1', 'LENG8-AS1', 'DDX39B-AS1', 'FAM181A-AS1', 'ITPK1-AS1',
'SERTAD4-AS1', 'ZFY-AS1', 'GLIS2-AS1', 'ZNF436-AS1', 'EPHA1-AS1', 'MCPH1-AS1', 'SLC14A2-AS1',
'DHRS4-AS1', 'PPP4R1-AS1', 'C1RL-AS1', 'AQP4-AS1', 'MCM8-AS1', 'SIRPG-AS1', 'TTC39C-AS1',
'ISM1-AS1', 'MACROD2-AS1', 'TTC3-AS1', 'ASMTL-AS1', 'CACNA1C-AS4', 'CACNA1C-AS2',
'KCNK15-AS1', 'USP12-AS2', 'ARHGAP5-AS1', 'STK4-AS1', 'PAN3-AS1', 'HORMAD2-AS1',
'TEX26-AS1', 'SLC25A21-AS1', 'DLGAP1-AS3', 'URB1-AS1', 'ZNF295-AS1', 'ZNF674-AS1',
'ITCH-AS1', 'EP300-AS1', 'FUT8-AS1', 'USP12-AS1', 'DIAPH3-AS1', 'MIS18A-AS1', 'PCDH9-AS4',
'NDFIP2-AS1', 'BRWD1-AS2', 'BRWD1-AS1', 'BMP7-AS1', 'STX18-AS1', 'PRR34-AS1', 'RBM26-AS1',
'FGF13-AS1', 'WASF3-AS1', 'DSG2-AS1', 'FOXN3-AS1', 'PCDH9-AS3', 'RAP2C-AS1', 'UCKL1-AS1',
'B4GALT1-AS1', 'TAPT1-AS1', 'ZNF337-AS1', 'CTBP1-AS', 'DIO2-AS1', 'TRPM2-AS', 'TSPEAR-AS1',
'TSPEAR-AS2', 'FRMD6-AS1', 'ST8SIA6-AS1', 'EFCAB6-AS1', 'FRMD6-AS2', 'PCCA-AS1', 'CDKN2B-AS1',
'SCEL-AS1', 'MCM3AP-AS1', 'ADORA2A-AS1', 'GPC5-AS2', 'LY86-AS1', 'PCDH9-AS1', 'PROSER2-AS1',
'TSC22D1-AS1', 'SGMS1-AS1', 'FAM83C-AS1', 'MORC2-AS1', 'PARD3-AS1', 'F10-AS1', 'JARID2-AS1',
'LNX1-AS1', 'FAM170B-AS1', 'ELOVL2-AS1', 'IGF2-AS', 'MGAT3-AS1', 'UBOX5-AS1', 'PAXBP1-AS1',
'ITGB2-AS1', 'HM13-AS1', 'ZNF503-AS2', 'GRID1-AS1', 'JMJD1C-AS1', 'PRMT5-AS1', 'KIZ-AS1',
'EDNRB-AS1', 'MACC1-AS1', 'ZNF341-AS1', 'NAV2-AS5', 'GPC6-AS1', 'FGF14-AS1', 'MORF4L2-AS1',
'SYP-AS1', 'FGF14-AS2', 'BDNF-AS', 'PLCG1-AS1', 'A2ML1-AS1', 'GABRG3-AS1', 'BTBD9-AS1',
'TRAM2-AS1', 'PPP1R26-AS1', 'SACS-AS1', 'RNASEH2B-AS1', 'PLBD1-AS1', 'SLC39A12-AS1', 'COL5A1-AS1',
'CSE1L-AS1', 'DSG1-AS1', 'OGFR-AS1', 'VPS13A-AS1', 'PRRX2-AS1', 'FAM53B-AS1', 'MCHR2-AS1', 'SNCA-AS1',
'WDFY3-AS1', 'NRSN2-AS1', 'DBH-AS1', 'IQCH-AS1', 'ARNTL2-AS1', 'THAP9-AS1', 'ADNP-AS1', 'SLC25A25-AS1',
'LZTS1-AS1', 'ZNRF3-AS1', 'ODF2-AS1', 'GAS6-AS1', 'HOXC-AS1', 'TEX36-AS1', 'FOCAD-AS1', 'RARA-AS1',
'LMO7-AS1', 'EDRF1-AS1', 'ZBTB46-AS1', 'TPT1-AS1', 'USP2-AS1', 'SLC25A30-AS1', 'GSN-AS1', 'IFT74-AS1',
'HTR2A-AS1', 'DIAPH3-AS2', 'ARAP1-AS2'"),
width = 5
)),
box(
title = "Top positive loaded comps", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
plotOutput("TopLoadComp_Plot"),
width = 5
),
box(
title = "Enrichment across components", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
plotOutput("TopLoadedBarplot"),
width = 10
),
box(
title = "Cor(loadings) of SDA components", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
downloadButton("CompCorCustPlot_download"),
plotOutput("CompCorCustPlot"),
width = 10
)
),
### lncRNA_expr_toploaded -----
tabItem(tabName = "lncRNA_expr_toploaded",
fluidRow(
box(
title = "Selection of component", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
textInput("ComponentNtext_lncRNATopLoaded", "SDA component search (numerical):", "1"),
# plotOutput("lncRNA_topLoaded"),
width = 5
),
box(
title = "Top Loaded lncRNAs Neg and Pos", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
textOutput("lncRNAgenes_Neg_txt"),
textOutput("lncRNAgenes_Pos_txt"),
width = 10
),
box(
title = "Overlap of lncRNAs (biomaRt 04/2022)", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
plotOutput("lncRNA_Venn"),
width = 5
),
box(
title = "Distribution of lncRNAs vs Random gene set", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
plotOutput("lncRNA_toploaded"),
width = 5
),
box(
title = "Enrichment across components", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
plotOutput("lncRNA_BarplotSDA"),
width = 10
)
# valueBoxOutput("lncRNAgenes", width = NULL),
)
),
### CompCor -----
tabItem(tabName = "CompCor",
fluidRow(
valueBoxOutput("CorPlot_CellType1", width = 3),
box(
title = "Cor(loadings) of SDA components", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
textInput("CompCorSDAnum", "Top 150 genes of SDA component (numerical):", "1"),
sliderInput(inputId = "CompCorSDAnum_ngene",
label = "Number of top genes:",
min = 10,
max = 150,
value = 24),
downloadButton("CompCorPlot_download"),
plotOutput("CompCorPlot"),
width = 10
),
box(
title = "Top Loaded genes", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
textOutput("top_Neg_txt"),
textOutput("top_Peg_txt"),
width = 10
)
)
),
### CompCor -----
tabItem(tabName = "GeneCor",
fluidRow(
# valueBoxOutput("CorPlot_CellType1", width = 3),
box(
radioButtons("celltypeselect_geneCor", "Celltype Selection:",
c("Leydig" = "leydig",
"Sertoli" = "sertoli",
"Myoid" = "myoid",
"Neuro" = "neuro",
"Germ-All" = "germ",
"Germ-UndiffSg" = "germ_UnDiffSgSct",
"Germ-DiffSg" = "germ_DiffSgSct",
"Germ-PrePachSct" = "germ_PrePachSct",
"Germ-PachSct" = "germ_PachSct",
"Germ_Std" = "germ_Std",
"Endothelial" = "endothelial",
"Myeloid" = "myeloid",
"Adaptive" = "adaptive",
"All" = "all"
), selected = "germ_UnDiffSgSct"),
width = 5
),
box(
title = "Cor(GEX) gene expression correlation", status = "primary", solidHeader = TRUE,
collapsible = TRUE,
textInput("GeneSet_geneCor", "A set of genes", "'NANOS1', 'NANOS2', 'NANOS3', 'DMRT1', 'KIT', 'PLPPR3', 'CCK', 'HES5', 'PLPPR5', 'RHCE', 'SCT', 'FAM25G', 'DPPA4', 'TDRD1', 'MAGEA4', 'STRA8', 'DPPA4', 'TDRD1', 'MAGEA4', 'STRA8', 'GFRA1', 'BCL6B', 'ID4', 'PIWIL4', 'DNMT1', 'DMRT1', 'KIT', 'DMC1', 'SYCP3', 'ETV5', 'EGR4'"),
downloadButton("GeneCorPlot_download"),
plotOutput("GeneCorPlot"),
width = 10
)
)
),
## External Data -----
### Soma only w LN19 -----
tabItem(tabName = "somaWLN",
h2("Reprocessing of: \nMahyari-Conrad et al. (2021) + \n Laurentino-Neuhaus (2019)*"),
fluidRow(
box(
title = "Phenotype", status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
downloadButton("tsnesomaonlywln_phenotype_download"),
plotOutput("tSNE_somaWLN_Pheno3_Rx"),
width = 5,
# footer = "* Laurentino et al. 2019 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6714305/"
),
box(
title = "Condition", status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
downloadButton("tsnesomaonlywln_condition_download"),
plotOutput("tSNE_somaWLN_COND.ID_Rx"),
width = 5,
# footer = "* Laurentino et al. 2019 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6714305/"
),
box(
title = "Donors", status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
downloadButton("tsnesomaonlywln_donor_download"),
plotOutput("tSNE_somaWLN_DONR.ID_Rx"),
width = 5,
footer = "* Laurentino et al. 2019 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6714305/"
),
box(
title = "Total No. of transcripts", status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
downloadButton("tsnesomaonlywln_ncount_download"),
plotOutput("tSNE_somaWLN_nCount_RNA_Rx"),
width = 5,
# footer = "* Laurentino et al. 2019 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6714305/"
)
)
),
### LC only w Zhao20 LN19 -----
tabItem(tabName = "LConly",
h2("Reprocessing of Leydig Cells (LC): \nMahyari-Conrad et al. (2021) + \n Laurentino-Neuhaus (2019) + \n Zhao-Li (2020)**"),
fluidRow(
box(
title = "Mahyari et al. only data", status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
# downloadButton("tsnesomaonlywln_donor_download"),
plotOutput("DimRedux_LConly_donors_Rx"),
width = 5,
#footer = "* Laurentino et al. 2019 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6714305/ \n** Zhao et al. 2020 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7655944/"
),
box(
title = "Mahyari et al. only data", status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
# downloadButton("tsnesomaonlywln_donor_download"),
plotOutput("DimRedux_LConly_phenotype_Rx"),
width = 5,
#footer = "* Laurentino et al. 2019 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6714305/ \n** Zhao et al. 2020 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7655944/"
),
box(
title = "LC from Mahyari21 + LN19 + Zhao20", status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
# downloadButton("tsnesomaonlywln_donor_download"),
plotOutput("DimRedux_LConlyZhao_donors_Rx"),
width = 5,
footer = "* Laurentino et al. 2019 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6714305/ \n** Zhao et al. 2020 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7655944/"
),
box(
title = "LC from Mahyari21 + LN19 + Zhao20", status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
# downloadButton("tsnesomaonlywln_donor_download"),
plotOutput("DimRedux_LConlyZhao_phenotype_Rx"),
width = 5,
#footer = "* Laurentino et al. 2019 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6714305/ \n** Zhao et al. 2020 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7655944/"
),
box(
title = "LC from Mahyari21 + LN19 + Zhao20", status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
# downloadButton("tsnesomaonlywln_donor_download"),
plotOutput("DimRedux_LConlyZhao_phenotypeProp_Rx"),
width = 5,
#footer = "* Laurentino et al. 2019 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6714305/ \n** Zhao et al. 2020 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7655944/"
),
box(
title = "LC from Mahyari21 + LN19 + Zhao20", status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
# downloadButton("tsnesomaonlywln_donor_download"),
plotOutput("DimRedux_LConlyZhao_KeyGenesViolin_Rx"),
width = 10,
#footer = "* Laurentino et al. 2019 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6714305/ \n** Zhao et al. 2020 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7655944/"
),
)
)
)#tabitems
)#dashboardBody
)#dashboardPage
# Server -----
server <- function(input, output, session) {
source("app_server.R",local = TRUE)
}
shinyApp(ui, server)
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