ui.R
In spell098/rnaseq_app:
library(shiny)
shinyUI(fluidPage(
titlePanel("Linear model 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, ""),
fileInput("File2", "Optional: Upload RNAseq module file"),
fileInput("File3", "Optional: Upload RNAseq reactions list"),
selectInput("specie","Specie",choices=c("hsapiens","rnorvegicus")),
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("selectedComparison", label = "Select the comparison of interest", choices = NULL),
selectInput("selectedVariables",label= "Select the variables to compare",choices=NULL,multiple=TRUE),
actionButton("submit1", "Run!"),
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")),
actionButton("submit2", "Update restriction parameters")
,witdth=2),
mainPanel(
helpText("test"),
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("Clustering",
numericInput("selectedClustn",label = "select number of clusters for summary",value=3),
dataTableOutput("summaryClustering"),
numericInput("pval_clust",label="select a p-value for significant clustering group",value=0.2),
plotOutput("plotCorrectAttribution"),
plotOutput("plotCorrectSubsample")
),
tabPanel("PCA",
sliderInput("cex.PCA", label = "Labels size of the PCA plot", min=0.5,max = 2, value = 1),
plotOutput("PCA",height="500px"),
sliderInput("cex.MDS", label = "Labels size of the MDS plot", min=0.5,max = 2, value = 1),
plotOutput("MDS")
),
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")
)
)
#N'arrive pas a afficher tous les graphique en loop
),
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",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",
tabsetPanel(
tabPanel("Results summary",
help('Download results all comparisons'),
downloadButton('downloadAllResults', 'Download'),
dataTableOutput("resultsSummary"),
downloadButton("downloadSummary","Download"),
tags$textarea(id = "selectedGene", placeholder = 'gene of interest', rows = 8, ""),
plotOutput("boxplot_element")
),
tabPanel("Results table",
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",
dataTableOutput("topGO"),
downloadButton("downloadTopGO","Download"),
tags$textarea(id = "selectedOntology", placeholder = 'ontologies of interest', rows = 8, ""),
dataTableOutput("selectedGO"),
downloadButton('downloadSelectedGO', 'Download'),
downloadButton('downloadNodeSelectedGO','Download nodes file for cytoscape'),
downloadButton('downloadEdgeSelectedGO','Download edges file for cytoscape')
),
tabPanel("Top modules",
actionButton("submitMethylModule","Calculate Modules"),
helpText("This action may take a while..."),
dataTableOutput("modulesTable"),
downloadButton("downloadModulesTable","Download"),
dataTableOutput("selectedModule"),
downloadButton("downloadSelectedModule","Download"),
dataTableOutput("topModuleGO"),
downloadButton("downloadtopModuleGO","Download"),
dataTableOutput("resultsModuleOntology"),
downloadButton("downloadResultsModuleOntology","Download")
),
tabPanel("Raw data",
#don't display the whole thing, it's useless; make the user enter is genes of interest manually, and display only that
tags$textarea(id = "selectedGenes", placeholder = 'genes of interest', rows = 8, ""),
dataTableOutput("rawTopTable"),
downloadButton("downloadRawTopTable","Download"),
plotOutput("boxplot_element_raw")
)
)
#verbatimTextOutput("results"),
),
tabPanel("Network Analysis",
textOutput("confirmFindReactions"),
numericInput("threshold","Adjacency threshold for network",value = 0.7),
actionButton("findTopReactions","Find top reactions"),
dataTableOutput("topReactions"),
tags$textarea(id = "selectedReactions", placeholder = 'Reactions of interest', rows = 3, ""),
#selectInput("selectedReactions", label = "Select pathways of interest", choices = NULL),
plotOutput("pathway",width="100%",height="800px"),
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",
dataTableOutput("topTableMethyl"),
downloadButton('downloadResultsMethyl', 'Download'),
downloadButton('downloadNodeDataComparisonMethyl','Download nodes file for cytoscape'),
downloadButton('downloadEdgeDataComparisonMethyl','Download edges file for cytoscape'),
dataTableOutput("topTableMethylOutGene"),
downloadButton('downloadResultsMethylOut', 'Download'),
downloadButton('downloadNodeDataComparisonMethylOutGene','Download nodes file for cytoscape'),
downloadButton('downloadEdgeDataComparisonMethylOutGene','Download edges file for cytoscape'),
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",
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),
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..."),
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),
dataTableOutput("selectedModuleMethyl")
),
tabPanel("Raw CpGs",
tags$textarea(id = "selectedCpgs", placeholder = 'CpGs of interest', rows = 8, ""),
dataTableOutput("rawTopCpG")
),
tabPanel("Raw methylated genes",
tags$textarea(id = "selectedCpgGenes", placeholder = 'Genes of interest', rows = 8, ""),
dataTableOutput("rawTopCpgGenes")
)
)
#verbatimTextOutput("results"),
),
tabPanel("Network Analysis",
textOutput("confirmFindReactions2"),
actionButton("findTopReactions2","Find top reactions"),
dataTableOutput("topReactions2"),
tags$textarea(id = "selectedReactions2", placeholder = 'Reactions of interest', rows = 3, ""),
#selectInput("selectedReactions", label = "Select pathways of interest", choices = NULL),
plotOutput("pathway2",width="100%",height="800px"),
dataTableOutput("toptableNodes2")
)
))
)
),
tabPanel("RNAseq / Methylation integration",
tabsetPanel(
tabPanel("CpG/RNA",
dataTableOutput("mergeTable")
),
tabPanel("Any CpG/RNA"
),
tabPanel("Network"
)
)
)
)))
spell098/rnaseq_app documentation built on May 30, 2019, 7:57 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
library(shiny)
shinyUI(fluidPage(
titlePanel("Linear model analysis"),
tabsetPanel(
tabPanel("RNA-seq",
sidebarLayout(
sidebarPanel(
helpText("Options"),
fileInput("File1", "Updload RNAseq data file"),
selectInput("fileContent","File Content",choices=c("Expression Matrix","Expression Set"),selected="Expression Matrix"),
tags$textarea(id = "geo_id", placeholder = 'GEO ID', rows = 1, ""),
fileInput("File2", "Optional: Upload RNAseq module file"),
fileInput("File3", "Optional: Upload RNAseq reactions list"),
selectInput("specie","Specie",choices=c("hsapiens","rnorvegicus")),
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("selectedComparison", label = "Select the comparison of interest", choices = NULL),
selectInput("selectedVariables",label= "Select the variables to compare",choices=NULL,multiple=TRUE),
actionButton("submit1", "Run!"),
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")),
actionButton("submit2", "Update restriction parameters")
,witdth=2),
mainPanel(
helpText("test"),
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("Clustering",
numericInput("selectedClustn",label = "select number of clusters for summary",value=3),
dataTableOutput("summaryClustering"),
numericInput("pval_clust",label="select a p-value for significant clustering group",value=0.2),
plotOutput("plotCorrectAttribution"),
plotOutput("plotCorrectSubsample")
),
tabPanel("PCA",
sliderInput("cex.PCA", label = "Labels size of the PCA plot", min=0.5,max = 2, value = 1),
plotOutput("PCA",height="500px"),
sliderInput("cex.MDS", label = "Labels size of the MDS plot", min=0.5,max = 2, value = 1),
plotOutput("MDS")
),
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")
)
)
#N'arrive pas a afficher tous les graphique en loop
),
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",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",
tabsetPanel(
tabPanel("Results summary",
help('Download results all comparisons'),
downloadButton('downloadAllResults', 'Download'),
dataTableOutput("resultsSummary"),
downloadButton("downloadSummary","Download"),
tags$textarea(id = "selectedGene", placeholder = 'gene of interest', rows = 8, ""),
plotOutput("boxplot_element")
),
tabPanel("Results table",
dataTableOutput("topTable"),
downloadButton('downloadResultsSelectedComparison', 'Download table'),
downloadButton('downloadNodeDataComparison','Download nodes file for cytoscape'),
downloadButton('downloadEdgeDataComparison','Download edges file for cytoscape'),
downloadButton("downloadColorMatrixResults","Download")
),
tabPanel("Venn",
sliderInput("lfc", label = "Select log Fold Change (logFC) limit (absolute)", value = c(1) ,max=5,min=0,step=0.05),
sliderInput("venn.cex", label = "Venn Diagram caracters size", max=2,min=0.5,value=1),
plotOutput("venn"),
downloadButton("downloadVenn","Download")
),
tabPanel("Top gene Ontologies",
dataTableOutput("topGO"),
downloadButton("downloadTopGO","Download"),
tags$textarea(id = "selectedOntology", placeholder = 'ontologies of interest', rows = 8, ""),
dataTableOutput("selectedGO"),
downloadButton('downloadSelectedGO', 'Download'),
downloadButton('downloadNodeSelectedGO','Download nodes file for cytoscape'),
downloadButton('downloadEdgeSelectedGO','Download edges file for cytoscape')
),
tabPanel("Top modules",
actionButton("submitMethylModule","Calculate Modules"),
helpText("This action may take a while..."),
dataTableOutput("modulesTable"),
downloadButton("downloadModulesTable","Download"),
dataTableOutput("selectedModule"),
downloadButton("downloadSelectedModule","Download"),
dataTableOutput("topModuleGO"),
downloadButton("downloadtopModuleGO","Download"),
dataTableOutput("resultsModuleOntology"),
downloadButton("downloadResultsModuleOntology","Download")
),
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$textarea(id = "selectedGenes", placeholder = 'genes of interest', rows = 8, ""),
dataTableOutput("rawTopTable"),
downloadButton("downloadRawTopTable","Download"),
plotOutput("boxplot_element_raw")
)
)
#verbatimTextOutput("results"),
),
tabPanel("Network Analysis",
textOutput("confirmFindReactions"),
numericInput("threshold","Adjacency threshold for network",value = 0.7),
actionButton("findTopReactions","Find top reactions"),
dataTableOutput("topReactions"),
tags$textarea(id = "selectedReactions", placeholder = 'Reactions of interest', rows = 3, ""),
#selectInput("selectedReactions", label = "Select pathways of interest", choices = NULL),
plotOutput("pathway",width="100%",height="800px"),
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",
dataTableOutput("topTableMethyl"),
downloadButton('downloadResultsMethyl', 'Download'),
downloadButton('downloadNodeDataComparisonMethyl','Download nodes file for cytoscape'),
downloadButton('downloadEdgeDataComparisonMethyl','Download edges file for cytoscape'),
dataTableOutput("topTableMethylOutGene"),
downloadButton('downloadResultsMethylOut', 'Download'),
downloadButton('downloadNodeDataComparisonMethylOutGene','Download nodes file for cytoscape'),
downloadButton('downloadEdgeDataComparisonMethylOutGene','Download edges file for cytoscape'),
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",
dataTableOutput("topGOMethyl")
),
tabPanel("Selected ontologies results",
numericInput("headGOMethyl", label = "Number of gene ontologies to display", value = 10),
tags$textarea(id = "selectedOntology", placeholder = 'ontologies of interest', rows = 8, ""),
#selectInput("selectedOntology",label = "Select ontologies of interest",choices = NULL),
numericInput("thresholdMethyl","Adjacency threshold for network",value = 0.7),
dataTableOutput("selectedGOMethyl"),
downloadButton('downloadSelectedGOMethyl', 'Download'),
downloadButton('downloadNodeSelectedGOMethyl','Download nodes file for cytoscape'),
downloadButton('downloadEdgeSelectedGOMethyl','Download edges file for cytoscape')
),
tabPanel("Top modules",
actionButton("submitMethylModule","Calculate Modules"),
helpText("This action may take a while..."),
dataTableOutput("moduleTableMethyl")
),
tabPanel("Selected modules results",
numericInput("headModuleMethyl", label = "Number of Modules to display", value = 20),
selectInput("selectedModuleMethyl", label = "Select the module of interest", choices = NULL, multiple=TRUE),
dataTableOutput("selectedModuleMethyl")
),
tabPanel("Raw CpGs",
tags$textarea(id = "selectedCpgs", placeholder = 'CpGs of interest', rows = 8, ""),
dataTableOutput("rawTopCpG")
),
tabPanel("Raw methylated genes",
tags$textarea(id = "selectedCpgGenes", placeholder = 'Genes of interest', rows = 8, ""),
dataTableOutput("rawTopCpgGenes")
)
)
#verbatimTextOutput("results"),
),
tabPanel("Network Analysis",
textOutput("confirmFindReactions2"),
actionButton("findTopReactions2","Find top reactions"),
dataTableOutput("topReactions2"),
tags$textarea(id = "selectedReactions2", placeholder = 'Reactions of interest', rows = 3, ""),
#selectInput("selectedReactions", label = "Select pathways of interest", choices = NULL),
plotOutput("pathway2",width="100%",height="800px"),
dataTableOutput("toptableNodes2")
)
))
)
),
tabPanel("RNAseq / Methylation integration",
tabsetPanel(
tabPanel("CpG/RNA",
dataTableOutput("mergeTable")
),
tabPanel("Any CpG/RNA"
),
tabPanel("Network"
)
)
)
)))
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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