Commit 60e00139 authored by Stevenn Volant's avatar Stevenn Volant
Browse files

modif diag plot + sere

parents 7e82168f 84440282
library(shinydashboard)
if (!require(rNVD3)) {
install.packages('rNVD3')
library(rNVD3)
if (!require("Rcpp")){
install.packages("Rcpp")
}
if(!require(shinydashboard)){
install.packages('shinydashboard')
library(shinydashboard)
}
if(!require(rjson)){
install.packages('rjson')
}
if(!require(devtools)){
install.packages('devtools')
}
<<<<<<< HEAD
=======
#library(plotly)
>>>>>>> 84440282f7e33f02d6a643f231ab33bf935f89c1
if (!require(psych)) {
install.packages('psych')
library(psych)
......@@ -31,6 +44,13 @@ if (!require(biom)) {
install.packages('biom')
library(biom)
}
if (!require(devtools)) {
install.packages('devtools')
}
if (!require(rNVD3)) {
library(devtools)
install_github('rNVD3', 'ramnathv')
}
source("internal.R")
renderDataTable <- DT::renderDataTable
......
......@@ -47,7 +47,7 @@ if (!require(DESeq2)) {
if (!require(ade4)) {
install.packages('ade4')
library(ade4)
}
}
sidebar <- dashboardSidebar(
sidebarMenu(
......@@ -69,7 +69,7 @@ the differential analysis and mutiple visualization.",style = "font-family: 'tim
Resulting p-values are adjusted according to the Benjamini and Hochberg procedure [Benjamini and Hochberg 1995].
The PCOA is performed with the", a("ade4 R package",href="http://pbil.univ-lyon1.fr/ade4/"), "and plots are generated with", a("ggplot2",href="http://ggplot2.org/"), "or", a("D3.js packages",href="http://d3js.org/"), ".", style = "font-family: 'times'; font-si16pt")),
tabPanel("Authors", h3("The main contributors to Meta16s:"),
p(a("Stevenn Volant", href="mailto:stevenn.volant@pasteur.fr"), "(Initiator, coding, testing, documentation, evaluation)"),
p(a("Stevenn Volant", href="mailto:stevenn.volant"), "(Initiator, coding, testing, documentation, evaluation)"),
p(a("Amine Ghozlane",href="mailto:amine.ghozlane@pasteur.fr"), "(Coding, testing, documentation, feature suggestions)"),
p(a("Pierre Lechat",href="mailto:pierre.lechat@pasteur.fr"), "(Coding, testing, feature suggestions)"),
p(a("Marie-Agnès Dillies",href="mailto:marie-agnes.dillies@pasteur.fr"), "(Evaluation)"),
......@@ -200,9 +200,9 @@ The PCOA is performed with the", a("ade4 R package",href="http://pbil.univ-lyon1
tabItem(tabName = "DiagPlotTab",
fluidRow(
column(width=9,
plotOutput("PlotDiag",height="100%"),
br(),
box(title = "Plot", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
plotOutput("PlotDiag")
),
conditionalPanel(condition="input.DiagPlot=='SfactorsVStot'",
box(title = "Size factors", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
dataTableOutput("SizeFactTable")
......@@ -211,12 +211,12 @@ The PCOA is performed with the", a("ade4 R package",href="http://pbil.univ-lyon1
conditionalPanel(condition="input.DiagPlot=='pcaPlot'",
box(title = "Eigen values", width = 6, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
plotOutput("PlotEigen",height="100%")
plotOutput("PlotEigen")
)
),
conditionalPanel(condition="input.DiagPlot=='pcoaPlot'",
box(title = "Eigen values", width = 6, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
plotOutput("PlotpcoaEigen",height="100%")
plotOutput("PlotpcoaEigen")
)
)
......@@ -233,14 +233,11 @@ The PCOA is performed with the", a("ade4 R package",href="http://pbil.univ-lyon1
conditionalPanel(condition="input.DiagPlot!='Sfactors' && input.DiagPlot!='SfactorsVStot' ",uiOutput("VarIntDiag")),
conditionalPanel(condition="input.DiagPlot=='pcoaPlot'",
h5(strong("Select the modalities")),
uiOutput("ModMat")
),
conditionalPanel(condition="input.DiagPlot=='pcoaPlot' || input.DiagPlot=='SERE' || input.DiagPlot=='clustPlot' ",
selectInput("DistClust","Distance",c("euclidean", "SERE"="sere", "canberra", "bray", "kulczynski", "jaccard",
"gower", "altGower", "morisita", "horn","mountford","raup","binomial",
"chao","cao","mahalanobis"),selected="jaccard")
uiOutput("ModMat"),
selectInput("DistPCOA","Distance",c("euclidean", "canberra", "bray", "kulczynski", "jaccard",
"gower", "altGower", "morisita", "horn","mountford","raup","binomial",
"chao","cao","mahalanobis"),selected="jaccard")
)
# conditionalPanel(condition="input.RadioPlotBi=='Nuage'",selectInput("ColorBiplot", "Couleur",choices=c("Bleue" = 'blue',"Rouge"='red',"Vert"='green', "Noir"='black'),width="50%")),
# sliderInput("TransAlphaBi", "Transparence",min=1, max=100, value=50, step=1),
# conditionalPanel(condition="input.RadioPlotBi!='Nuage'", radioButtons("SensGraphBi","Sens du graph",choices=c("Vertical"="Vert","Horizontal"="Hori"))),
......@@ -252,8 +249,6 @@ The PCOA is performed with the", a("ade4 R package",href="http://pbil.univ-lyon1
# h6(strong("Layout")),
# numericInput("NbcolSfactors", h6("Columns"),min=1,value = NA)
# ),
sliderInput("heightDiag", "Height",min=100,max=1500,value = 500,step =10),
conditionalPanel(condition="input.DiagPlot=='clustPlot'",
h6(strong("Layout")),
selectInput("typeHculst", h6("Type"),c("Horizontal"="hori","Fan"="fan")),
......@@ -266,16 +261,8 @@ The PCOA is performed with the", a("ade4 R package",href="http://pbil.univ-lyon1
sliderInput("cexstar", "Star height",min=0,max=1,value = 0.95,step =0.1)
),
conditionalPanel(condition="input.DiagPlot=='SfactorsVStot'",
checkboxInput("addLabelSFact","Add label",FALSE)
),
fluidRow(
column(width=12, p(strong("Size"))),
column(width=6,sliderInput("cexTitleDiag", h6("Axis"),min=0,max=5,value = 1,step =0.1)),
conditionalPanel(condition="input.DiagPlot=='SfactorsVStot' || input.DiagPlot=='pcaPlot'",column(width=6,sliderInput("cexLabelDiag", h6("Points"),min=0,max=5,value = 1,step =0.1)))
)
sliderInput("cexLabelDiag", "Label size",min=0,max=5,value = 1,step =0.1)
# sliderInput("heightDiag", "height",min=100,max=1500,value = 500,step =10),
# sliderInput("widthDiag", "width",min=100,max=1500,value = 1000,step =10)
......
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