ui.R
In spell098/rnaseq_functions2: Contain various functions for rnaseq analysis
library(shiny)
shinyUI(fluidPage(
titlePanel("RNAseq analysis"),
tabsetPanel(
tabPanel("RNA-seq",
sidebarLayout(
sidebarPanel(
helpText("Options"),
fileInput("File1", "Updload RNAseq data file"),
selectInput("fileContent","File Content",choices=c("Expression Matrix","Expression Set"), selected="Expression Matrix"),
tags$textarea(id = "geo_id", placeholder = 'GEO ID', rows = 1, "GSE54839"),
fileInput("File2", "Optional: Upload RNAseq module file"),
fileInput("File3", "Optional: Upload RNAseq reactions list"),
radioButtons("randomSamples",label=h5("Use a sample of whole dataset"),choices=list("True" = "TRUE","False"="FALSE"),selected=FALSE),
numericInput("randomSampling","Select number of random elements to use",value=1000),
actionButton("submitRun", "Load"),
selectInput("standardization","Standardization method",choices = c("no","none", "scale", "quantile", "Aquantile", "Gquantile", "Rquantile", "Tquantile", "vsn", "cyclicloess"), selected="no"),
selectInput("specie","Specie",choices=c("hsapiens","rnorvegicus")),
selectInput("mart","Mart type",choices=c("ENSEMBL_MART_ENSEMBL","ENSEMBL_MART_SNP","ENSEMBL_MART_FUNCGEN","ENSEMBL_MART_VEGA","pride")),
radioButtons("type",label=h5("transcript or gene results?"),choices=list("Genes" = "ensembl_gene_id","Transcripts"="ensembl_transcript_id")),
tags$textarea(id = "attribute", placeholder = 'Type of ID e.g. affy_hg_u95av2', rows = 3, "illumina_humanht_12_v3"),
selectInput("groupBy",label="Make group by",choices=c("groups","fuzzy"),selected="groups"),
numericInput("noCluster",label= "Number of clusters for fuzzy c-means clustering",value=3),
selectInput("selectedVariables",label= "Select the variables to compare",choices=NULL,multiple=TRUE),
selectInput("selectedReplicates", label = "Replicates informations", choices = NULL,multiple=TRUE),
selectInput("selectedComparison", label = "Select the comparison of interest", choices = NULL),
actionButton("submitParam","Update dataset parameters"),
actionButton("submitModule","Calculate Modules"),
numericInput("pow","Power for WGCNA",value=6),
helpText("This action may take a while..."),
numericInput("pvalue", label = "Select a p-value",value = 0.01,max=1,min=0),
numericInput("logFCneg", label = "Select the negative logFC limit", value = -1.3),
numericInput("logFCpos", label = "Select the positive logFC limit", value = 1.3),
selectInput("adjust",label="p-value correction method",selected="BH",choices=c("no","none","BH","BY","holm")),
selectInput("ordination","Select the type of ordination",choices=c("Principal Component Analysis","Redundency analysis","correspondence analysis","detrended correspondence analysis","non-metric multidimensional scaling")),
actionButton("submit2", "Run!"),
#actionButton("findSignificantModules","Find Significant Modules"),
actionButton("submitNetwork", "Network Analysis")
,witdth=2),
mainPanel(
textOutput("warnings"),
textOutput("text1"),
tabsetPanel(
tabPanel("Quality Control",
tabsetPanel(
tabPanel("Boxplot",
sliderInput("cex.axis_boxplot",label = "Caracters size on the axis",min=0,max=1,value=0.6),
sliderInput("ylim",label = "Limits of the y-axis", min = -30, max = 30, value = c(-15, 15),step=0.1),
plotOutput("boxplot"),
help('Save data with new groups'),
downloadButton("downloadExprMatrix","Download data")
),
tabPanel("Comparisons Table",
DT::dataTableOutput("comparisons_table")
),
tabPanel("Clustering",
actionButton("submitSummaryClust","Generate clustering summary tables"),
numericInput("selectedClustn",label = "select number of clusters for summary",value=3),
DT::dataTableOutput("summaryClustering"),
numericInput("pval_clust",label="select a p-value for significant clustering group",value=0.2),
plotOutput("plotCorrectAttribution"),
plotOutput("plotCorrectSubsample")
)
)
#N'arrive pas a afficher tous les graphique en loop
),
tabPanel("Ordination",
tabsetPanel(
tabPanel("Ordination",
radioButtons("random",label=h5("Use a sample of whole dataset"),choices=list("True" = "TRUE","False"="FALSE"),selected=FALSE),
numericInput("randomSamplingOrd","Select number of random elements to use",value=1000),
actionButton("submitOrdination","Generate ordination analysis"),
sliderInput("cex.PCA", label = "Labels size of the plot", min=0.5,max = 2, value = 1),
plotOutput("ordination",height="500px"),
sliderInput("cex.MDS", label = "Labels size of the MDS plot", min=0.5,max = 2, value = 1),
plotOutput("MDS")
),
tabPanel("Principal Components top genes",
DT::dataTableOutput("eigenvalues"),
DT::dataTableOutput("u"),
DT::dataTableOutput("v"),
DT::dataTableOutput("ordinationAnova"),
plotOutput("boxplot_element_pca"),
numericInput("bins","Nunmber of columns",value=20),
plotOutput("hist_element_pca"),
selectInput("topOrdinationGenes","Principal Componant of interest",choices=NULL)
),
tabPanel("Heatmaps",
selectInput("dendrogram", label = "Dendrograms",choices = c("column","row","both","none"),selected = "none"),
selectInput("scale", label = "Scale", choices = c("column","row"), selected="row"),
sliderInput("cexRow_heatmap_ord",label = "Caracters size on the x-axis",min=0,max=1.5,value=0.5),
sliderInput("row_heatmap_height_ord",label = "Row height",min=0,max=6,value=2,step=0.05),
tabsetPanel(
tabPanel("Individual samples",
plotOutput("heatmap1_ord",width="100%",height="1000px")
),
tabPanel("Grouped samples",
plotOutput("heatmap2_ord",width="100%",height="1000px")
)
)
),
tabPanel("Top gene Ontologies",
DT::dataTableOutput("topGO_ord"),
downloadButton("downloadTopGO_ord","Download"),
tags$textarea(id = "selectedOntology_ord", placeholder = 'ontologies of interest', rows = 8, ""),
DT::dataTableOutput("selectedGO_ord"),
downloadButton('downloadSelectedGO_ord', 'Download'),
downloadButton('downloadNodeSelectedGO_ord','Download nodes file for cytoscape'),
downloadButton('downloadEdgeSelectedGO_ord','Download edges file for cytoscape')
),
tabPanel("Module analysis",
DT::dataTableOutput("modulesTableOrd"),
#downloadButton("downloadModulesTable","Download"),
tabsetPanel(
tabPanel("Genes of interest",
DT::dataTableOutput("selectedModule3"),
#downloadButton("downloadSelectedModulePCA","Download"),
DT::dataTableOutput("topModuleGO3"),
#downloadButton("downloadtopPCAModuleGO","Download"),
DT::dataTableOutput("resultsModuleOntology3")
#downloadButton("downloadResultsModulePCAOntology","Download")
),
tabPanel("Module analysis",
DT::dataTableOutput("selectedModule4"),
#downloadButton("downloadModuleTable","Download"),
DT::dataTableOutput("topModuleGO4"),
#downloadButton("downloadtopModuleGO","Download"),
DT::dataTableOutput("resultsModuleOntology4")
#downloadButton("downloadResultsModuleTableOntology","Download")
)
)
)
)
),
tabPanel("Differential analysis results",
tabsetPanel(
tabPanel("Volcano & MA plots",
numericInput("pvalueVolcano",label = "p-val for volcano plot",value = 0.05),
numericInput("logFCVolcano",label = "Absolute logFC for volcano plot", value = 1),
plotOutput("volcanoplot"),
plotOutput("MA")
),
tabPanel("Heatmaps",
selectInput("dendrogram", label = "Dendrograms",choices = c("column","row","both","none"),selected = "both"),
selectInput("scale", label = "Scale", choices = c("column","row"), selected="row"),
sliderInput("cexRow_heatmap",label = "Caracters size on the x-axis",min=0,max=1.5,value=0.5),
sliderInput("row_heatmap_height",label = "Row height",min=0,max=6,value=2,step=0.05),
tabsetPanel(
tabPanel("Individual samples",
plotOutput("heatmap1",width="100%",height="1000px")
),
tabPanel("Grouped samples",
plotOutput("heatmap2",width="100%",height="1000px")
),
tabPanel("Comparison heatmap",
sliderInput("heatdiagram_cex",label = "Cex heatdiagram",min=0,max=3,value=0.6,step=0.05),
plotOutput("heatDiagram",width="100%",height="1000px")
)
)
) ,
tabPanel("Results summary",
help('Download results all comparisons'),
downloadButton('downloadAllResults', 'Download'),
DT::dataTableOutput("resultsSummary"),
downloadButton("downloadSummary","Download"),
plotOutput("boxplot_element"),
plotOutput("hist_element")
),
#Mettre ensembl results table, gene ontology et network. Faire apparaitre graph boxplot / chaque table
tabPanel("Results table",
DT::dataTableOutput("topTable"),
downloadButton('downloadResultsSelectedComparison', 'Download table'),
downloadButton('downloadNodeDataComparison','Download nodes file for cytoscape'),
downloadButton('downloadEdgeDataComparison','Download edges file for cytoscape'),
downloadButton("downloadColorMatrixResults","Download")
),
tabPanel("Venn",
sliderInput("lfc", label = "Select log Fold Change (logFC) limit (absolute)", value = c(1) ,max=5,min=0,step=0.05),
sliderInput("venn.cex", label = "Venn Diagram caracters size", max=2,min=0.5,value=1),
plotOutput("venn"),
downloadButton("downloadVenn","Download")
),
tabPanel("Top gene Ontologies",
DT::dataTableOutput("topGO"),
downloadButton("downloadTopGO","Download"),
tags$textarea(id = "selectedOntology", placeholder = 'ontologies of interest', rows = 8, ""),
DT::dataTableOutput("selectedGO"),
downloadButton('downloadSelectedGO', 'Download'),
downloadButton('downloadNodeSelectedGO','Download nodes file for cytoscape'),
downloadButton('downloadEdgeSelectedGO','Download edges file for cytoscape')
),
tabPanel("Top modules",
DT::dataTableOutput("modulesTable"),
#downloadButton("downloadModulesTable","Download"),
tabsetPanel(
tabPanel("Genes of interest",
DT::dataTableOutput("selectedModule1"),
#downloadButton("downloadSelectedModule","Download"),
DT::dataTableOutput("topModuleGO1"),
#downloadButton("downloadtopModuleGO","Download"),
DT::dataTableOutput("resultsModuleOntology1")
#downloadButton("downloadResultsModuleOntology","Download")
),
tabPanel("Module analysis",
DT::dataTableOutput("selectedModule2"),
#downloadButton("downloadModuleTable","Download"),
DT::dataTableOutput("topModuleGO2"),
#downloadButton("downloadtopModuleGO","Download"),
DT::dataTableOutput("resultsModuleOntology2")
#downloadButton("downloadResultsModuleTableOntology","Download")
)
)
),
tabPanel("top ordination genes",
DT::dataTableOutput("diffOrd"),
DT::dataTableOutput("resultsOrdDiff"),
DT::dataTableOutput("topOrdDiffGO"),
DT::dataTableOutput("resultsOrdDiffOntology")
),
tabPanel("Raw data",
#don't display the whole thing, it's useless; make the user enter is genes of interest manually, and display only that
tags$textarea(id = "selectedGenes", placeholder = 'genes of interest', rows = 8, ""),
DT::dataTableOutput("rawTopTable"),
downloadButton("downloadRawTopTable","Download"),
plotOutput("boxplot_element_raw")
)
)
),
tabPanel("Network Analysis",
textOutput("confirmFindReactions"),
numericInput("threshold","Adjacency threshold for network",value = 0.7),
actionButton("findTopReactions","Find top reactions"),
DT::dataTableOutput("topReactions"),
tags$textarea(id = "selectedReactions", placeholder = 'Reactions of interest', rows = 3, ""),
plotOutput("pathway",width="100%",height="800px"),
DT::dataTableOutput("pathwayTable")
)
))
) ),
tabPanel("Methylation",
sidebarLayout(
sidebarPanel(
helpText("Option"),
fileInput("File5", "Updload metylation table file"),
fileInput("File6", "Updload metylation results file"),
fileInput("File7", "Optional: Upload methylation module file"),
fileInput("File8", "Optional: Upload methylation reactions list"),
selectInput("specieEnsembl","specieEnsembl",choices=c("rnorvegicus_gene_ensembl","hsapiens_gene_ensembl")),
selectInput("symbol","Type of gene symbols",choices=c("rgd_symbol","hgnc_symbol")),
selectInput("selectedComparisonMethyl", label = "Select the comparison of interest", choices = NULL),
selectInput("selectedVariablesMethyl",label= "Select the variables to compare",choices=NULL,multiple=TRUE),
actionButton("submit21", "Run!"),
numericInput("methDiffNeg", label = "Select negative limit",value = -25),
numericInput("methDiffPos", label = "Select positive limit",value = 25),
numericInput("qvalue", label = "Select a q-value",value = 0.01,max=1,min=0),
actionButton("submit22", "Update restriction parameters")
,witdth=2),
mainPanel(
textOutput("test2"),
textOutput("test3"),
actionButton("submit23","Calculate differential analysis!"),
tabsetPanel(
tabPanel("Quality Control",
tabsetPanel(
tabPanel("Boxplot",
sliderInput("cex.axis_boxplot2",label = "Caracters size on the axis",min=0,max=1,value=0.6),
sliderInput("ylim2",label = "Limits of the y-axis", min = 0, max = 1, value = c(0, 1),step=0.1),
plotOutput("boxplot2")
),
tabPanel("MDS",
sliderInput("cex.MDS", label = "Labels size of the MDS plot", min=0.5,max = 2, value = 1),
plotOutput("MDS2"),
plotOutput("PCA2")
),
tabPanel("Volcanoplots",
plotOutput("volcanoplot2")
),
tabPanel("Correlation",
plotOutput("correlation")
),
tabPanel("Tree",
plotOutput("tree")
)
)
#N'arrive pas a afficher tous les graphique en loop
),
tabPanel("Heatmaps",
selectInput("dendrogram2", label = "Dendrograms",choices = c("column","row","both","none"),selected = "none"),
selectInput("scale2", label = "Scale", choices = c("column","row"), selected="row"),
sliderInput("cexRow_heatmap2",label = "Caracters size on the x-axis",min=0,max=1.5,value=0.5),
sliderInput("row_heatmap_height2",label = "Row height",min=0,max=6,value=2,step=0.05),
tabsetPanel(
tabPanel("Individual samples",
plotOutput("heatmap21",width="100%",height="1000px")
),
tabPanel("Grouped samples",
plotOutput("heatmap22",width="100%",height="1000px")
),
tabPanel("Comparison heatmap",
sliderInput("heatdiagram_cex",label = "Cex heatdiagram",min=0,max=3,value=0.6,step=0.05),
plotOutput("heatDiagram2",width="100%",height="1000px")
)
)
) ,
tabPanel("Results",
tabsetPanel(
tabPanel("Results table",
DT::dataTableOutput("topTableMethyl"),
downloadButton('downloadResultsMethyl', 'Download'),
downloadButton('downloadNodeDataComparisonMethyl','Download nodes file for cytoscape'),
downloadButton('downloadEdgeDataComparisonMethyl','Download edges file for cytoscape'),
DT::dataTableOutput("topTableMethylOutGene"),
downloadButton('downloadResultsMethylOut', 'Download'),
downloadButton('downloadNodeDataComparisonMethylOutGene','Download nodes file for cytoscape'),
downloadButton('downloadEdgeDataComparisonMethylOutGene','Download edges file for cytoscape'),
DT::dataTableOutput("cpgByGene"),
downloadButton('downloadResultsByGene', 'Download'),
downloadButton('downloadNodeDataComparisonMethylByGene','Download nodes file for cytoscape'),
downloadButton('downloadEdgeDataComparisonMethylByGene','Download edges file for cytoscape')
),
tabPanel("Venn",
sliderInput("lfcMethyl", label = "Select log Fold Change (logFC) limit (absolute)", value = c(1) ,max=5,min=0,step=0.05),
sliderInput("venn.cexMethyl", label = "Venn Diagram caracters size", max=2,min=0.5,value=1),
plotOutput("vennMethyl")
),
tabPanel("Top gene Ontologies",
DT::dataTableOutput("topGOMethyl")
),
tabPanel("Selected ontologies results",
numericInput("headGOMethyl", label = "Number of gene ontologies to display", value = 10),
tags$textarea(id = "selectedOntology", placeholder = 'ontologies of interest', rows = 8, ""),
#selectInput("selectedOntology",label = "Select ontologies of interest",choices = NULL),
numericInput("thresholdMethyl","Adjacency threshold for network",value = 0.7),
DT::dataTableOutput("selectedGOMethyl"),
downloadButton('downloadSelectedGOMethyl', 'Download'),
downloadButton('downloadNodeSelectedGOMethyl','Download nodes file for cytoscape'),
downloadButton('downloadEdgeSelectedGOMethyl','Download edges file for cytoscape')
),
tabPanel("Top modules",
actionButton("submitMethylModule","Calculate Modules"),
helpText("This action may take a while..."),
DT::dataTableOutput("moduleTableMethyl")
),
tabPanel("Selected modules results",
numericInput("headModuleMethyl", label = "Number of Modules to display", value = 20),
selectInput("selectedModuleMethyl", label = "Select the module of interest", choices = NULL, multiple=TRUE),
DT::dataTableOutput("selectedModuleMethyl")
),
tabPanel("Raw CpGs",
tags$textarea(id = "selectedCpgs", placeholder = 'CpGs of interest', rows = 8, ""),
DT::dataTableOutput("rawTopCpG")
),
tabPanel("Raw methylated genes",
tags$textarea(id = "selectedCpgGenes", placeholder = 'Genes of interest', rows = 8, ""),
DT::dataTableOutput("rawTopCpgGenes")
)
)
),
tabPanel("Network Analysis",
textOutput("confirmFindReactions2"),
actionButton("findTopReactions2","Find top reactions"),
DT::dataTableOutput("topReactions2"),
tags$textarea(id = "selectedReactions2", placeholder = 'Reactions of interest', rows = 3, ""),
#selectInput("selectedReactions", label = "Select pathways of interest", choices = NULL),
plotOutput("pathway2",width="100%",height="800px"),
DT::dataTableOutput("toptableNodes2")
)
))
)
),
tabPanel("RNAseq / Methylation integration",
tabsetPanel(
tabPanel("CpG/RNA",
DT::dataTableOutput("mergeTable")
),
tabPanel("Any CpG/RNA"
),
tabPanel("Network"
)
)
)
)))
spell098/rnaseq_functions2 documentation built on May 30, 2019, 7:57 a.m.
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library(shiny)
shinyUI(fluidPage(
titlePanel("RNAseq analysis"),
tabsetPanel(
tabPanel("RNA-seq",
sidebarLayout(
sidebarPanel(
helpText("Options"),
fileInput("File1", "Updload RNAseq data file"),
selectInput("fileContent","File Content",choices=c("Expression Matrix","Expression Set"), selected="Expression Matrix"),
tags$textarea(id = "geo_id", placeholder = 'GEO ID', rows = 1, "GSE54839"),
fileInput("File2", "Optional: Upload RNAseq module file"),
fileInput("File3", "Optional: Upload RNAseq reactions list"),
radioButtons("randomSamples",label=h5("Use a sample of whole dataset"),choices=list("True" = "TRUE","False"="FALSE"),selected=FALSE),
numericInput("randomSampling","Select number of random elements to use",value=1000),
actionButton("submitRun", "Load"),
selectInput("standardization","Standardization method",choices = c("no","none", "scale", "quantile", "Aquantile", "Gquantile", "Rquantile", "Tquantile", "vsn", "cyclicloess"), selected="no"),
selectInput("specie","Specie",choices=c("hsapiens","rnorvegicus")),
selectInput("mart","Mart type",choices=c("ENSEMBL_MART_ENSEMBL","ENSEMBL_MART_SNP","ENSEMBL_MART_FUNCGEN","ENSEMBL_MART_VEGA","pride")),
radioButtons("type",label=h5("transcript or gene results?"),choices=list("Genes" = "ensembl_gene_id","Transcripts"="ensembl_transcript_id")),
tags$textarea(id = "attribute", placeholder = 'Type of ID e.g. affy_hg_u95av2', rows = 3, "illumina_humanht_12_v3"),
selectInput("groupBy",label="Make group by",choices=c("groups","fuzzy"),selected="groups"),
numericInput("noCluster",label= "Number of clusters for fuzzy c-means clustering",value=3),
selectInput("selectedVariables",label= "Select the variables to compare",choices=NULL,multiple=TRUE),
selectInput("selectedReplicates", label = "Replicates informations", choices = NULL,multiple=TRUE),
selectInput("selectedComparison", label = "Select the comparison of interest", choices = NULL),
actionButton("submitParam","Update dataset parameters"),
actionButton("submitModule","Calculate Modules"),
numericInput("pow","Power for WGCNA",value=6),
helpText("This action may take a while..."),
numericInput("pvalue", label = "Select a p-value",value = 0.01,max=1,min=0),
numericInput("logFCneg", label = "Select the negative logFC limit", value = -1.3),
numericInput("logFCpos", label = "Select the positive logFC limit", value = 1.3),
selectInput("adjust",label="p-value correction method",selected="BH",choices=c("no","none","BH","BY","holm")),
selectInput("ordination","Select the type of ordination",choices=c("Principal Component Analysis","Redundency analysis","correspondence analysis","detrended correspondence analysis","non-metric multidimensional scaling")),
actionButton("submit2", "Run!"),
#actionButton("findSignificantModules","Find Significant Modules"),
actionButton("submitNetwork", "Network Analysis")
,witdth=2),
mainPanel(
textOutput("warnings"),
textOutput("text1"),
tabsetPanel(
tabPanel("Quality Control",
tabsetPanel(
tabPanel("Boxplot",
sliderInput("cex.axis_boxplot",label = "Caracters size on the axis",min=0,max=1,value=0.6),
sliderInput("ylim",label = "Limits of the y-axis", min = -30, max = 30, value = c(-15, 15),step=0.1),
plotOutput("boxplot"),
help('Save data with new groups'),
downloadButton("downloadExprMatrix","Download data")
),
tabPanel("Comparisons Table",
DT::dataTableOutput("comparisons_table")
),
tabPanel("Clustering",
actionButton("submitSummaryClust","Generate clustering summary tables"),
numericInput("selectedClustn",label = "select number of clusters for summary",value=3),
DT::dataTableOutput("summaryClustering"),
numericInput("pval_clust",label="select a p-value for significant clustering group",value=0.2),
plotOutput("plotCorrectAttribution"),
plotOutput("plotCorrectSubsample")
)
)
#N'arrive pas a afficher tous les graphique en loop
),
tabPanel("Ordination",
tabsetPanel(
tabPanel("Ordination",
radioButtons("random",label=h5("Use a sample of whole dataset"),choices=list("True" = "TRUE","False"="FALSE"),selected=FALSE),
numericInput("randomSamplingOrd","Select number of random elements to use",value=1000),
actionButton("submitOrdination","Generate ordination analysis"),
sliderInput("cex.PCA", label = "Labels size of the plot", min=0.5,max = 2, value = 1),
plotOutput("ordination",height="500px"),
sliderInput("cex.MDS", label = "Labels size of the MDS plot", min=0.5,max = 2, value = 1),
plotOutput("MDS")
),
tabPanel("Principal Components top genes",
DT::dataTableOutput("eigenvalues"),
DT::dataTableOutput("u"),
DT::dataTableOutput("v"),
DT::dataTableOutput("ordinationAnova"),
plotOutput("boxplot_element_pca"),
numericInput("bins","Nunmber of columns",value=20),
plotOutput("hist_element_pca"),
selectInput("topOrdinationGenes","Principal Componant of interest",choices=NULL)
),
tabPanel("Heatmaps",
selectInput("dendrogram", label = "Dendrograms",choices = c("column","row","both","none"),selected = "none"),
selectInput("scale", label = "Scale", choices = c("column","row"), selected="row"),
sliderInput("cexRow_heatmap_ord",label = "Caracters size on the x-axis",min=0,max=1.5,value=0.5),
sliderInput("row_heatmap_height_ord",label = "Row height",min=0,max=6,value=2,step=0.05),
tabsetPanel(
tabPanel("Individual samples",
plotOutput("heatmap1_ord",width="100%",height="1000px")
),
tabPanel("Grouped samples",
plotOutput("heatmap2_ord",width="100%",height="1000px")
)
)
),
tabPanel("Top gene Ontologies",
DT::dataTableOutput("topGO_ord"),
downloadButton("downloadTopGO_ord","Download"),
tags$textarea(id = "selectedOntology_ord", placeholder = 'ontologies of interest', rows = 8, ""),
DT::dataTableOutput("selectedGO_ord"),
downloadButton('downloadSelectedGO_ord', 'Download'),
downloadButton('downloadNodeSelectedGO_ord','Download nodes file for cytoscape'),
downloadButton('downloadEdgeSelectedGO_ord','Download edges file for cytoscape')
),
tabPanel("Module analysis",
DT::dataTableOutput("modulesTableOrd"),
#downloadButton("downloadModulesTable","Download"),
tabsetPanel(
tabPanel("Genes of interest",
DT::dataTableOutput("selectedModule3"),
#downloadButton("downloadSelectedModulePCA","Download"),
DT::dataTableOutput("topModuleGO3"),
#downloadButton("downloadtopPCAModuleGO","Download"),
DT::dataTableOutput("resultsModuleOntology3")
#downloadButton("downloadResultsModulePCAOntology","Download")
),
tabPanel("Module analysis",
DT::dataTableOutput("selectedModule4"),
#downloadButton("downloadModuleTable","Download"),
DT::dataTableOutput("topModuleGO4"),
#downloadButton("downloadtopModuleGO","Download"),
DT::dataTableOutput("resultsModuleOntology4")
#downloadButton("downloadResultsModuleTableOntology","Download")
)
)
)
)
),
tabPanel("Differential analysis results",
tabsetPanel(
tabPanel("Volcano & MA plots",
numericInput("pvalueVolcano",label = "p-val for volcano plot",value = 0.05),
numericInput("logFCVolcano",label = "Absolute logFC for volcano plot", value = 1),
plotOutput("volcanoplot"),
plotOutput("MA")
),
tabPanel("Heatmaps",
selectInput("dendrogram", label = "Dendrograms",choices = c("column","row","both","none"),selected = "both"),
selectInput("scale", label = "Scale", choices = c("column","row"), selected="row"),
sliderInput("cexRow_heatmap",label = "Caracters size on the x-axis",min=0,max=1.5,value=0.5),
sliderInput("row_heatmap_height",label = "Row height",min=0,max=6,value=2,step=0.05),
tabsetPanel(
tabPanel("Individual samples",
plotOutput("heatmap1",width="100%",height="1000px")
),
tabPanel("Grouped samples",
plotOutput("heatmap2",width="100%",height="1000px")
),
tabPanel("Comparison heatmap",
sliderInput("heatdiagram_cex",label = "Cex heatdiagram",min=0,max=3,value=0.6,step=0.05),
plotOutput("heatDiagram",width="100%",height="1000px")
)
)
) ,
tabPanel("Results summary",
help('Download results all comparisons'),
downloadButton('downloadAllResults', 'Download'),
DT::dataTableOutput("resultsSummary"),
downloadButton("downloadSummary","Download"),
plotOutput("boxplot_element"),
plotOutput("hist_element")
),
#Mettre ensembl results table, gene ontology et network. Faire apparaitre graph boxplot / chaque table
tabPanel("Results table",
DT::dataTableOutput("topTable"),
downloadButton('downloadResultsSelectedComparison', 'Download table'),
downloadButton('downloadNodeDataComparison','Download nodes file for cytoscape'),
downloadButton('downloadEdgeDataComparison','Download edges file for cytoscape'),
downloadButton("downloadColorMatrixResults","Download")
),
tabPanel("Venn",
sliderInput("lfc", label = "Select log Fold Change (logFC) limit (absolute)", value = c(1) ,max=5,min=0,step=0.05),
sliderInput("venn.cex", label = "Venn Diagram caracters size", max=2,min=0.5,value=1),
plotOutput("venn"),
downloadButton("downloadVenn","Download")
),
tabPanel("Top gene Ontologies",
DT::dataTableOutput("topGO"),
downloadButton("downloadTopGO","Download"),
tags$textarea(id = "selectedOntology", placeholder = 'ontologies of interest', rows = 8, ""),
DT::dataTableOutput("selectedGO"),
downloadButton('downloadSelectedGO', 'Download'),
downloadButton('downloadNodeSelectedGO','Download nodes file for cytoscape'),
downloadButton('downloadEdgeSelectedGO','Download edges file for cytoscape')
),
tabPanel("Top modules",
DT::dataTableOutput("modulesTable"),
#downloadButton("downloadModulesTable","Download"),
tabsetPanel(
tabPanel("Genes of interest",
DT::dataTableOutput("selectedModule1"),
#downloadButton("downloadSelectedModule","Download"),
DT::dataTableOutput("topModuleGO1"),
#downloadButton("downloadtopModuleGO","Download"),
DT::dataTableOutput("resultsModuleOntology1")
#downloadButton("downloadResultsModuleOntology","Download")
),
tabPanel("Module analysis",
DT::dataTableOutput("selectedModule2"),
#downloadButton("downloadModuleTable","Download"),
DT::dataTableOutput("topModuleGO2"),
#downloadButton("downloadtopModuleGO","Download"),
DT::dataTableOutput("resultsModuleOntology2")
#downloadButton("downloadResultsModuleTableOntology","Download")
)
)
),
tabPanel("top ordination genes",
DT::dataTableOutput("diffOrd"),
DT::dataTableOutput("resultsOrdDiff"),
DT::dataTableOutput("topOrdDiffGO"),
DT::dataTableOutput("resultsOrdDiffOntology")
),
tabPanel("Raw data",
#don't display the whole thing, it's useless; make the user enter is genes of interest manually, and display only that
tags$textarea(id = "selectedGenes", placeholder = 'genes of interest', rows = 8, ""),
DT::dataTableOutput("rawTopTable"),
downloadButton("downloadRawTopTable","Download"),
plotOutput("boxplot_element_raw")
)
)
),
tabPanel("Network Analysis",
textOutput("confirmFindReactions"),
numericInput("threshold","Adjacency threshold for network",value = 0.7),
actionButton("findTopReactions","Find top reactions"),
DT::dataTableOutput("topReactions"),
tags$textarea(id = "selectedReactions", placeholder = 'Reactions of interest', rows = 3, ""),
plotOutput("pathway",width="100%",height="800px"),
DT::dataTableOutput("pathwayTable")
)
))
) ),
tabPanel("Methylation",
sidebarLayout(
sidebarPanel(
helpText("Option"),
fileInput("File5", "Updload metylation table file"),
fileInput("File6", "Updload metylation results file"),
fileInput("File7", "Optional: Upload methylation module file"),
fileInput("File8", "Optional: Upload methylation reactions list"),
selectInput("specieEnsembl","specieEnsembl",choices=c("rnorvegicus_gene_ensembl","hsapiens_gene_ensembl")),
selectInput("symbol","Type of gene symbols",choices=c("rgd_symbol","hgnc_symbol")),
selectInput("selectedComparisonMethyl", label = "Select the comparison of interest", choices = NULL),
selectInput("selectedVariablesMethyl",label= "Select the variables to compare",choices=NULL,multiple=TRUE),
actionButton("submit21", "Run!"),
numericInput("methDiffNeg", label = "Select negative limit",value = -25),
numericInput("methDiffPos", label = "Select positive limit",value = 25),
numericInput("qvalue", label = "Select a q-value",value = 0.01,max=1,min=0),
actionButton("submit22", "Update restriction parameters")
,witdth=2),
mainPanel(
textOutput("test2"),
textOutput("test3"),
actionButton("submit23","Calculate differential analysis!"),
tabsetPanel(
tabPanel("Quality Control",
tabsetPanel(
tabPanel("Boxplot",
sliderInput("cex.axis_boxplot2",label = "Caracters size on the axis",min=0,max=1,value=0.6),
sliderInput("ylim2",label = "Limits of the y-axis", min = 0, max = 1, value = c(0, 1),step=0.1),
plotOutput("boxplot2")
),
tabPanel("MDS",
sliderInput("cex.MDS", label = "Labels size of the MDS plot", min=0.5,max = 2, value = 1),
plotOutput("MDS2"),
plotOutput("PCA2")
),
tabPanel("Volcanoplots",
plotOutput("volcanoplot2")
),
tabPanel("Correlation",
plotOutput("correlation")
),
tabPanel("Tree",
plotOutput("tree")
)
)
#N'arrive pas a afficher tous les graphique en loop
),
tabPanel("Heatmaps",
selectInput("dendrogram2", label = "Dendrograms",choices = c("column","row","both","none"),selected = "none"),
selectInput("scale2", label = "Scale", choices = c("column","row"), selected="row"),
sliderInput("cexRow_heatmap2",label = "Caracters size on the x-axis",min=0,max=1.5,value=0.5),
sliderInput("row_heatmap_height2",label = "Row height",min=0,max=6,value=2,step=0.05),
tabsetPanel(
tabPanel("Individual samples",
plotOutput("heatmap21",width="100%",height="1000px")
),
tabPanel("Grouped samples",
plotOutput("heatmap22",width="100%",height="1000px")
),
tabPanel("Comparison heatmap",
sliderInput("heatdiagram_cex",label = "Cex heatdiagram",min=0,max=3,value=0.6,step=0.05),
plotOutput("heatDiagram2",width="100%",height="1000px")
)
)
) ,
tabPanel("Results",
tabsetPanel(
tabPanel("Results table",
DT::dataTableOutput("topTableMethyl"),
downloadButton('downloadResultsMethyl', 'Download'),
downloadButton('downloadNodeDataComparisonMethyl','Download nodes file for cytoscape'),
downloadButton('downloadEdgeDataComparisonMethyl','Download edges file for cytoscape'),
DT::dataTableOutput("topTableMethylOutGene"),
downloadButton('downloadResultsMethylOut', 'Download'),
downloadButton('downloadNodeDataComparisonMethylOutGene','Download nodes file for cytoscape'),
downloadButton('downloadEdgeDataComparisonMethylOutGene','Download edges file for cytoscape'),
DT::dataTableOutput("cpgByGene"),
downloadButton('downloadResultsByGene', 'Download'),
downloadButton('downloadNodeDataComparisonMethylByGene','Download nodes file for cytoscape'),
downloadButton('downloadEdgeDataComparisonMethylByGene','Download edges file for cytoscape')
),
tabPanel("Venn",
sliderInput("lfcMethyl", label = "Select log Fold Change (logFC) limit (absolute)", value = c(1) ,max=5,min=0,step=0.05),
sliderInput("venn.cexMethyl", label = "Venn Diagram caracters size", max=2,min=0.5,value=1),
plotOutput("vennMethyl")
),
tabPanel("Top gene Ontologies",
DT::dataTableOutput("topGOMethyl")
),
tabPanel("Selected ontologies results",
numericInput("headGOMethyl", label = "Number of gene ontologies to display", value = 10),
tags$textarea(id = "selectedOntology", placeholder = 'ontologies of interest', rows = 8, ""),
#selectInput("selectedOntology",label = "Select ontologies of interest",choices = NULL),
numericInput("thresholdMethyl","Adjacency threshold for network",value = 0.7),
DT::dataTableOutput("selectedGOMethyl"),
downloadButton('downloadSelectedGOMethyl', 'Download'),
downloadButton('downloadNodeSelectedGOMethyl','Download nodes file for cytoscape'),
downloadButton('downloadEdgeSelectedGOMethyl','Download edges file for cytoscape')
),
tabPanel("Top modules",
actionButton("submitMethylModule","Calculate Modules"),
helpText("This action may take a while..."),
DT::dataTableOutput("moduleTableMethyl")
),
tabPanel("Selected modules results",
numericInput("headModuleMethyl", label = "Number of Modules to display", value = 20),
selectInput("selectedModuleMethyl", label = "Select the module of interest", choices = NULL, multiple=TRUE),
DT::dataTableOutput("selectedModuleMethyl")
),
tabPanel("Raw CpGs",
tags$textarea(id = "selectedCpgs", placeholder = 'CpGs of interest', rows = 8, ""),
DT::dataTableOutput("rawTopCpG")
),
tabPanel("Raw methylated genes",
tags$textarea(id = "selectedCpgGenes", placeholder = 'Genes of interest', rows = 8, ""),
DT::dataTableOutput("rawTopCpgGenes")
)
)
),
tabPanel("Network Analysis",
textOutput("confirmFindReactions2"),
actionButton("findTopReactions2","Find top reactions"),
DT::dataTableOutput("topReactions2"),
tags$textarea(id = "selectedReactions2", placeholder = 'Reactions of interest', rows = 3, ""),
#selectInput("selectedReactions", label = "Select pathways of interest", choices = NULL),
plotOutput("pathway2",width="100%",height="800px"),
DT::dataTableOutput("toptableNodes2")
)
))
)
),
tabPanel("RNAseq / Methylation integration",
tabsetPanel(
tabPanel("CpG/RNA",
DT::dataTableOutput("mergeTable")
),
tabPanel("Any CpG/RNA"
),
tabPanel("Network"
)
)
)
)))
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