R/ShinnyApp.R
In camilleroquencourt/ptairMS: Pre-processing PTR-TOF-MS Data
Defines functions
RunShinnyApp
score_plotly
plotPeakRaw
Documented in
RunShinnyApp
utils::globalVariables(c("time", "intensity", "sd", "filter","cps","x","z",
"intensities","timeC","files"))
plotPeakRaw<-function(set,file, mzRange, peaks, temporalEstim,fctFit,
ppm = 2000,
palette = c("heat")[1]) {
if (length(mzRange) == 1)
mzRange <- mzRange + c(-1, 1) * mzRange * ppm * 1e-06
mz <- rhdf5::h5read(file, name = "FullSpectra/MassAxis")
mzRange[1] <- max(min(mz), mzRange[1], na.rm = TRUE)
mzRange[2] <- min(max(mz), mzRange[2], na.rm = TRUE)
# get the index of the aroud mzRange
index <- which(mzRange[1] < mz & mz < mzRange[2])
# object data
object <- rhdf5::h5read(file, name = "/FullSpectra/TofData",
index = list(index, NULL, NULL, NULL))
# time axis
timeVn <- as.numeric(names(getTimeInfo(set)$TIC[[basename(file)]]))
# calibrate mass axis
FirstcalibCoef <- try(rhdf5::h5read(file, "FullSpectra/MassCalibration",
index = list(NULL,1)))
attributCalib <- try(rhdf5::h5readAttributes(file, "/FullSpectra"))
if (!is.null(attr(FirstcalibCoef, "condition")) & is.null(attr(attributCalib, "condition"))) {
FirstcalibCoef <- matrix(c(attributCalib$`MassCalibration a`, attributCalib$`MassCalibration b`),
ncol = 1)
}
tof <- sqrt(mz) * FirstcalibCoef[1, 1] + FirstcalibCoef[2, 1]
# tof<- seq(0,length(mz))
coefCalib <- getCalibrationInfo(set)$coefCalib[[basename(file)]][[1]]
mzVn <- ((tof - coefCalib["b", ])/coefCalib["a", ])^2
mzVn <- mzVn[index]
# formate object matix
rawSubMN <- matrix(object, nrow = dim(object)[1],
ncol = prod(utils::tail(dim(object), 2)))
rawSubMN <- rawSubMN[,seq_len(length(timeVn)),drop=FALSE]
imageMN<-rawSubMN
dimnames(imageMN) <- list(mzVn, timeVn)
## chr: Current
bin<-diff(timeVn)[1]
chromVn <- apply(rawSubMN, 2, function(intVn) sum(intVn, na.rm = TRUE)/bin )
temporal <- ggplot2::ggplot() +
ggplot2::geom_point(data=data.frame(time=timeVn,cps=chromVn),
mapping = ggplot2::aes(x=time,y=cps)) + ggplot2::theme_classic()
temporal<-temporal + ggplot2::geom_line(data=data.frame(time=timeVn,cps=temporalEstim),
mapping = ggplot2::aes(x=time,y=cps))
## sca: Color scale
df <- data.frame(x = 1, y = seq_len(236), z = seq_len(236))
sca <- ggplot2::ggplot(df, ggplot2::aes(x, y)) +
ggplot2::geom_tile(ggplot2::aes(fill = z), size = 5) +
ggplot2::labs(x = NULL, y = NULL)+
ggplot2::scale_x_continuous(expand = c(0, 0)) +
ggplot2::scale_y_continuous(expand = c(0, 0))+
ggplot2::scale_fill_gradientn(colours = rev(grDevices::rainbow(100, end = 4/6)))
## ima: Image
rawM<-ggplot2::ggplot()
data<-data.frame(time=rep(timeVn,each=nrow(imageMN)),
mz=rep(as.numeric(rownames(imageMN)),ncol(imageMN)),
intensity=c(imageMN))
rawM <- ggplot2::ggplot() +
ggplot2::geom_tile(data=data, mapping=ggplot2::aes(time, mz, fill= intensity),show.legend =FALSE) +
ggplot2::scale_fill_gradientn(colours = rev(grDevices::rainbow(100, end = 4/6)))+
ggplot2::theme_classic()+
ggplot2::scale_x_continuous(expand = c(0, 0)) +
ggplot2::scale_y_continuous(expand = c(0, 0))+
ggplot2::theme(plot.title = ggplot2::element_blank(),
axis.title.x = ggplot2::element_text(size =12 ),
axis.title.y = ggplot2::element_text(size = 12),
axis.text = ggplot2::element_text(size = 10),
legend.title = ggplot2::element_text(size = 12),
legend.text = ggplot2::element_text( size = 10),
plot.caption = ggplot2::element_text(hjust = 0.5,size = 13) )
## spe: Spectrum
timeiNTER<-diff(timeVn)[1]
specVn <- apply(rawSubMN, 1, function(intVn) mean(intVn, na.rm = TRUE))
spctr<- ggplot2::ggplot()+
ggplot2::geom_point(data=data.frame(mz=as.numeric(rownames(imageMN)),intensities=specVn),
mapping = ggplot2::aes(x=mz,y=intensities)) + ggplot2::theme_classic()+
ggplot2::coord_flip()
spctr<- spctr + ggplot2::geom_line(data=data.frame(mz=as.numeric(rownames(imageMN)),
y=peaks( as.numeric(rownames(imageMN)) )),
mapping=ggplot2::aes(x=mz,y=y))
(ggpubr::ggarrange(
ggpubr::ggarrange(temporal,rawM,nrow=2,ncol=1,align = "v",heights=c(0.25,0.75)),
ggpubr::ggarrange(sca,spctr,nrow=2,ncol=1,heights=c(0.25,0.75)),
widths=c(0.75,0.25),ncol=2,nrow=1))
}
score_plotly <- function(ropls.model,label.c = "sampleNames",color.c = "",info.vc = "all",
title.c = "", components.vi = c(1, 2),palette.c = "Set1",ellipse.l = TRUE,
size.ls = list(axis_lab.i = 16,
axis_text.i = 14,
point.i = 3,
label.i = 5,
title.i = 20,
legend_title.i = 15,
legend_text.i = 15),
figure.c = c("interactive",
"interactive_plotly",
"my_scoreplot.pdf",
"my_scoreplot.html")[2])
{
# checking arguments and preparing data ----
## dataset [ExpressionSet] ----
eset <- ropls::getEset(ropls.model)
if (any(dim(eset) < 1))
stop("ExpressionSet object could not be extracted from the 'ropls.model'")
pdata.df <- Biobase::pData(eset)
#pdata.df$date<-as.factor(pdata.df$date)
data.df <- cbind.data.frame(sampleNames = Biobase::sampleNames(eset),
pdata.df,
stringsAsFactors = FALSE)
## plotly info ----
if (length(info.vc) == 1 && info.vc == "all") {
text.df <- data.df
} else {
info_in_metadata.vl <- info.vc %in% colnames(data.df)
if (any(!info_in_metadata.vl)) {
if (all(!info_in_metadata.vl)) {
stop("None of the selected info.vc names was found in the sampleMetadata:\n",
paste(info.vc, collapse = ", "))
} else {
warning("The following columns were not found in the sampleMetadata:\n",
paste(info.vc[!info_in_metadata.vl], collapse = ", "))
}
}
text.df <- data.df[, info.vc[info_in_metadata.vl], drop = FALSE]
}
text.vc <- apply(text.df, 1,
function(row.vc)
paste(paste0(colnames(text.df), " = ", row.vc), collapse = "\n"))
## score vectors ----
score.mn <- ropls::getScoreMN(ropls.model)
data.df <- cbind.data.frame(data.df,
text = text.vc,
score.mn)
## labels ----
#stopifnot(length(label.c) == 1)
if (label.c != "")
stopifnot(label.c %in% colnames(data.df))
## colors ----
#stopifnot(length(color.c) == 1)
if (color.c != "") {
stopifnot(color.c %in% colnames(data.df))
if (is.factor(data.df[, color.c]) || is.character(data.df[, color.c])) {
color_type.c <- "qualitative"
} else
color_type.c <- "quantitative"
}
## components ----
stopifnot(length(components.vi) == 2)
stopifnot(max(components.vi) <= ncol(score.mn))
## sizes ----
size_default.vi <- c(axis_lab.i = 16,
axis_text.i = 14,
point.i = 3,
label.i = 5,
title.i = 20,
legend_title.i = 15,
legend_text.i = 15)
for (size.c in names(size_default.vi)) {
if (!(size.c %in% names(size.ls)))
size.ls[[size.c]] <- size_default.vi[size.c]
}
## filename extention
filename_ext.c <- utils::tail(unlist(strsplit(basename(figure.c), ".", fixed = TRUE)), 1)
# starting the plot [ggplot]
p <- eval(parse(text = paste0("ggplot2::ggplot(data.df, ggplot2::aes(x = ",
paste0('p', components.vi[1]),
", y = ",
paste0('p', components.vi[2]),
ifelse(color.c != "",
paste0(", color = ", color.c),
""),
ifelse(label.c != "",
paste0(", label = ", label.c),
""),
", text = text))")))
## text/points [geom_text/geom_point] ----
if (label.c != "") {
p <- p + ggplot2::geom_text(size = size.ls[["label.i"]], ggplot2::aes(fontface = "bold"))
} else {
p <- p + ggplot2::geom_point(size = size.ls[["point.i"]])
}
## horizontal and vertical lines [geom_hline, geom_vline] ----
p <- p + ggplot2::geom_hline(ggplot2::aes(yintercept = 0)) +
ggplot2::geom_vline(ggplot2::aes(xintercept = 0))
## ellipses [stat_ellipse] ----
p <- p + eval(parse(text = paste0("ggplot2::stat_ellipse(ggplot2::aes(x = ",
paste0('p', components.vi[1]),
", y = ",
paste0('p', components.vi[2]),
", group = 1), type = 'norm')")))
if (ellipse.l && color.c != "" && color_type.c == "qualitative")
p <- p + eval(parse(text = paste0("ggplot2::stat_ellipse(ggplot2::aes(x = ",
paste0('p', components.vi[1]),
", y = ",
paste0('p', components.vi[2]),
", group = ",
ifelse(color.c != "", color.c, 1),
"), type = 'norm')")))
# title and axis labels [labs]
p <- p + ggplot2::labs(title = title.c,
x = paste0("t", components.vi[1],
" (",
round(ropls.model@modelDF[components.vi[1], "R2X"] * 100),
"%)"),
y = paste0("t", components.vi[2],
" (",
round(ropls.model@modelDF[components.vi[2], "R2X"] * 100),
"%)"))
# theme [them_bw, theme]
p <- p + ggplot2::theme_bw() +
ggplot2::theme(plot.title = ggplot2::element_text(size = size.ls[["title.i"]], face = "bold"),
axis.title.x = ggplot2::element_text(size = size.ls[["axis_lab.i"]], face = "bold"),
axis.title.y = ggplot2::element_text(size = size.ls[["axis_lab.i"]], face = "bold"),
axis.text = ggplot2::element_text(size = size.ls[["axis_text.i"]]),
legend.title = ggplot2::element_text(face = "bold", size = size.ls[["legend_title.i"]]),
legend.text = ggplot2::element_text(face = "bold", size = size.ls[["legend_text.i"]]))
# palette [scale_colour_brewer, scale_colour_gradientn]
if (color.c != "") {
if (color_type.c == "qualitative") {
if (palette.c != "")
p <- p + ggplot2::scale_colour_brewer(palette = palette.c)
} else
p <- p + ggplot2::scale_colour_gradientn(colours = rev(grDevices::rainbow(100, end = 4/6)))
}
# display/saving [plotly::ggplotly, plotly::layout, htmlwidgets::saveWidget, plotly::as_widget]
if (figure.c == "interactive_plotly" || filename_ext.c == "html") {
p <- plotly::ggplotly(p, tooltip = "text")
p <- plotly::layout(p, hoverlabel = list(font = list(size = 20)))
if (filename_ext.c == "html") {
#htmlwidgets::saveWidget(plotly::as_widget(p), figure.c)
return(p)
} else {
#print(p)
return(p)
}
} else {
if (filename_ext.c == "pdf")
grDevices::pdf(figure.c)
#print(p)
if (filename_ext.c == "pdf")
grDevices::dev.off()
return(p)
}
}
################# ui -----
#' Graphical interface of ptairMS workflow
#'
#' The whole workflow of ptairMS can be run interactively through a graphical user interface,
#' which provides visualizations (expiration phases, peaks in the raw data, peak table, individual VOCs),
#' quality controls (calibration, resolution, peak shape and evolution of reagent ions depending on time),
#' and exploratory data analysis.
#' @return Shinny app
#' @examples
#' \dontrun{RunShinnyApp()}
#' @rdname RunShinnyApp
#' @export
RunShinnyApp<-function(){
#' @importFrom shinyscreenshot screenshotButton
ui <- shiny::navbarPage("ptairMS",
# Application title
#titlePanel("ptairMS"),
#tabsetPanel(type = "tabs",
shiny::tabPanel("Read and check data",
shiny::fluidPage(
shiny::h3("Create/Load a PtrSet a from directory"),
shiny::selectInput("createOrLoad", "Choose action", c("loadPtrSet","createPtrSet"),
multiple=FALSE),
shiny::uiOutput("param")
),
##UI Affichage du Ptrset ----
shiny::sidebarLayout(
shiny::sidebarPanel(
shiny::h3("Your PtrSet:"),
shiny::verbatimTextOutput("showPtrSet",placeholder = FALSE),
shiny::uiOutput("update")
),
##UI tracé du PtrSet ----
shiny::mainPanel(
shiny::plotOutput("plotPtrSet"))),
##UI Calibration ----
shiny::sidebarLayout(
shiny::sidebarPanel(
shiny::h3("Calibration"),
shiny::uiOutput("paramCalib"),
shiny::uiOutput("paramCalib2"),
shiny::uiOutput("paramCalib3"),
shiny::uiOutput("paramCalib4"),
shiny::uiOutput("addMass_UI"),
# shiny::uiOutput("addMass")
),
shiny::mainPanel(
shiny::plotOutput("plotCalib"))),
shiny::sidebarLayout(
shiny::sidebarPanel(
shiny::h3("Expirations phases"),
# shiny::uiOutput("nomFile"),
shiny::uiOutput("paramTimeLimit")
),
shiny::mainPanel(
shiny::splitLayout(
DT::dataTableOutput("tableTimeLimit"),
plotly::plotlyOutput("plotTimeLimit")
))
),
shiny::fluidPage(
shinyscreenshot::screenshotButton()
)
),
shiny::tabPanel("Detect peak",
shiny::fluidRow(shiny::h3("Detect peak")),
shiny::fluidRow(
shiny::column( shiny::numericInput("PPM","min ppm sepration",130,0,200,10),width = 3),
shiny::column(shiny::numericInput("minIntensity","min intensity (cps)",5,0,200,10),width = 3),
shiny::column(shiny::numericInput("resMin ","resolution min",2000,0,20000,1000),width = 3),
shiny::column(shiny::numericInput("resMean ","resolution mean",5000,0,20000,1000),width = 3),
shiny::column(shiny::numericInput("resMax","resolution max",10000,0,20000,1000),width = 3)
),
shiny::fluidRow(
shiny::column( shiny::actionButton("detectPeak", "Detect peaks"),align="center",width = 12)
),
shiny::sidebarLayout(
shiny::sidebarPanel(
shiny::h3("Single file visualization"),
shiny::uiOutput("secondSelectionFileRawData"),
shiny::uiOutput("secondSelectionMzRawData")
),
#Plot
shiny::mainPanel(shiny::plotOutput("RawData"))
),
shiny::fluidPage(
shinyscreenshot::screenshotButton()
)
),
shiny::tabPanel("Align samples",
# alignement
# alignement
shiny::sidebarLayout(
shiny::sidebarPanel(
shiny::fluidPage(
shiny::h3("Alignment between samples"),
shiny::selectInput("quantiUnit","Unit:", c("ppb", "ncps", "cps"),selectize=FALSE),
shiny::numericInput("fracGroup","Maximum percentage of missing values per features",value = 0.3,min = 0,max = 1,step = 0.1),
shiny::uiOutput("group"),
shiny::numericInput("fracExp",
"Minimum percentage of samples such that features should be significativly
diffrent from ambiant air:",value = 0.1,min = 0,max = 1,step = 0.1),
shiny::numericInput("pValThres",
"The minimum p-value of the test between ambiant air and expirations:",value = 0.005,min = 0,max = 1,step = 0.1),
shiny::fluidRow(
shiny::column(width = 4, shiny::actionButton('align', 'Align samples')),
shiny::column(width = 4,shiny::verbatimTextOutput("nbPeak",placeholder = TRUE)),
shiny::column(width = 4,shiny::actionButton('export',"Export"))),
shiny::selectInput("Transformation","Matrix transformation:",c("log2","Centred reduced","None"),
selected = FALSE),
shiny::fluidRow(
shiny::column(width = 6, shiny::actionButton("impute", label = "Impute")),
shiny::column(width = 6,shiny::actionButton("outlier","Delete outlier")))
), width = 5),
# Show a plot of the generated distribution
shiny::mainPanel( plotly::plotlyOutput("tableAlign"), width = 7)),
shiny::sidebarLayout(
shiny::sidebarPanel(
shiny::h3("Metadata"),
shiny::uiOutput("secondSelectionLongitudinal")
),
# Show a plot of the generated distribution
shiny::mainPanel(plotly::plotlyOutput("dataLongitudinal"))
),
shiny::fluidPage(
shinyscreenshot::screenshotButton()
)
),
shiny::tabPanel("Statistical analysis",
shiny::fluidRow(
shiny::sidebarPanel(
shiny::h3("Principal Component Analysis"),
shiny::numericInput("x","Principal component of x-axis",1,1,4,1),
shiny::numericInput("y","Principal component of y-axis",2,1,4,1),
shiny::uiOutput("pca"),
shiny::uiOutput("pcaMarker")
),
# Show a plot of the generated distribution
shiny::mainPanel( plotly::plotlyOutput("acp"))
),
shiny::fluidRow(
shiny::sidebarPanel(
shiny::h3("Loading: features order by contribution"),
shiny::numericInput("maxRow","Number of row to display",10,1,100,1)
),
shiny::mainPanel(shiny::tableOutput("getLoading"))
),
shiny::fluidPage(
shinyscreenshot::screenshotButton()
)
)
#)
)
# Define server logic required to draw a histogram ----
server <- function(input, output) {
paramRv<-shiny::reactiveValues(path=NULL)
rv <- shiny::reactiveValues(ptrset=NULL, data=NULL,bgPoints=NULL,new=FALSE,file=NULL,newFile=TRUE)
## UI création d'un PtrSet ----
output$param<- shiny::renderUI({
if(input$createOrLoad == "createPtrSet"){
rv$new=TRUE
shiny::fluidPage(
shiny::fluidRow(
shiny::column(3,shiny::actionButton("selectDir","Select a directory")),
shiny::column(6,shiny::verbatimTextOutput(outputId = "showDirectorySelect",
placeholder = TRUE)),
shiny::column(3,shiny::textInput(inputId = "ptrName",label = "set name"))),
shiny::fluidRow(shiny::h4("Calibration masses"),
shiny::column(4,shiny::numericInput(inputId = "mz1",label = "mz1",value = 21.022)),
shiny::column(4,shiny::numericInput(inputId = "mz2",label = "mz2",value = 29.013424)),
shiny::column(4,shiny::numericInput(inputId = "mz3",label = "mz3",value = 60.0525)),
shiny::column(4,shiny::numericInput(inputId = "mz4",label = "mz4",value = 203.943)),
shiny::column(4,shiny::numericInput(inputId = "mz5",label = "mz5",value = 330.8495))),
shiny::fluidRow(
shiny::column(6,shiny::checkboxGroupInput(inputId = "BoolExp",
label = "Detect expirations phases",
choiceNames = c("TRUE"), choiceValues = c(TRUE))),
shiny::column(6,shiny::numericInput(inputId = "mzBreathTracer",label = "mzBreathTracer",value = 59.049))
),
#saveDir
shiny::fluidRow(
shiny::p(class = 'text-center',
shiny::actionButton(inputId = "createPtrSet",label = "create a PtrSet")
))
)
} else {
shiny::fluidRow(
shiny::p(class = 'text-center',
shiny::actionButton("selectFile","Choose a .Rdata ptrSet object"))
)
}
})
### Choose a directory ----
shiny::observeEvent(input$selectDir, {
pth <- utils::choose.dir() #tk_choose.dir
paramRv$path<-pth
})
### Display the choosen directory ----
output$showDirectorySelect<-shiny::renderPrint({
if(!is.null(paramRv$path)) print(paramRv$path)
})
### Création d'un directory si selection de createPtrSet ----
shiny::observeEvent(input$createPtrSet, {
if(!is.null(input$BoolExp)) fracMaxTIC<-0.7 else fracMaxTIC <- 0
ptrSet<-createPtrSet(dir = paramRv$path , setName = input$ptrName,
mzCalibRef = c(input$mz1,input$mz2,input$mz3,input$mz4,input$mz5),
fracMaxTIC = fracMaxTIC,
mzBreathTracer = input$mzBreathTracer, saveDir = paramRv$path)
rv$ptrset<-ptrSet
rv$new <-TRUE
})
shiny::observeEvent(input$selectFile, {
pth <- file.choose()
load_obj <- function(f){
env <- new.env()
nm <- load(f, env)[1]
env[[nm]]
}
rv$ptrset<-load_obj(pth)
rv$new <- TRUE
})
## Serveur Affichage du Ptrset ----
output$showPtrSet<-shiny::renderPrint(
if(!is.null(rv$ptrset)) print(rv$ptrset)
)
## Serveur Tracé du Ptrset ----
output$plotPtrSet <- shiny::renderPlot({
if(!is.null(rv$ptrset)) plot(rv$ptrset)
})
## Fonction serveur bouton Update Ptrset
output$update<- shiny::renderUI({
if(!is.null(rv$ptrset)) shiny::actionButton(inputId = "updatePtrSet",label = "Update ptrSet")
})
shiny::observeEvent(input$updatePtrSet,{
if(!is.null(rv$ptrset)){
rv$ptrset<-updatePtrSet(rv$ptrset)
rv$new <-TRUE
}
})
##UI output "paramTimeLimit" lorsque on a un ptrset ----
output$paramTimeLimit<-shiny::renderUI({
if(!is.null(rv$ptrset)){
shiny::fluidPage(
#choose file in the ptrSet
shiny::fluidRow(
if (rv$new){
shiny::selectInput("fileName","File name:",as.list(names(getTimeInfo(rv$ptrset)$TIC)),selected = FALSE,selectize=FALSE)
}
else {
shiny::selectInput("fileName","File name:",as.list(names(getTimeInfo(rv$ptrset)$TIC)),selected = input$fileName ,selectize=FALSE)
}
),
#UI rentrer les valeurs des paramètres
shiny::fluidRow(shiny::h5(shiny::strong("Parameters :"))),
# if (rv$newFile) {
# shiny::fluidRow(
#
# shiny::column(width = 6,shiny::numericInput("fracMaxTIC", "FracMaxTIC", 0.8 ,0, 1, 0.05)),
# shiny::column(width = 6,shiny::numericInput("fracMaxTICBg", "FracMaxTICBg",0.2,0, 1, 0.05)),
# shiny::column(width = 6,shiny::numericInput("derivThresholdExp", "DerivThresholdExp", 1, 0, 5, 0.05)),
# shiny::column(width = 6,shiny::numericInput("derivThresholdBg", "DerivThresholdBg",0.05,0, 2, 0.05)),
# shiny::column(width = 6,shiny::numericInput("minPoints", "MinPoints", 1, 1, 10, 1)),
# shiny::column(width = 6,shiny::numericInput("degreeBaseline", "DegreeBaseline", 1, 1, 30, 1)),
# shiny::column(width = 6,shiny::numericInput("knotsPeriod", "KnotsPeriod",
# 3, 1, 10, 1)),
# shiny::column(width = 10,shiny::selectInput(inputId = "methodKnot",
# label = "Method for knot location ",
# choices = c("Around expiration",
# "Uniform"),
# multiple = FALSE))
# )
# }
shiny::fluidRow(
shiny::column(width = 6,shiny::numericInput("fracMaxTIC", "FracMaxTIC", rv$ptrset@parameter$timeLimit$fracMaxTIC,0, 1, 0.05)),
shiny::column(width = 6,shiny::numericInput("fracMaxTICBg", "FracMaxTICBg",rv$ptrset@parameter$timeLimit$fracMaxTICBg,0, 1, 0.05)),
shiny::column(width = 6,shiny::numericInput("derivThresholdExp", "DerivThresholdExp", rv$ptrset@parameter$timeLimit$derivThresholdExp, 0, 5, 0.05)),
shiny::column(width = 6,shiny::numericInput("derivThresholdBg", "DerivThresholdBg",rv$ptrset@parameter$timeLimit$derivThresholdBg,0, 2, 0.05)),
shiny::column(width = 6,shiny::numericInput("minPoints", "MinPoints", rv$ptrset@parameter$timeLimit$minPoints, 1, 10, 1)),
shiny::column(width = 6,shiny::numericInput("degreeBaseline", "DegreeBaseline", rv$ptrset@parameter$timeLimit$degreeBaseline, 1, 30, 1)),
shiny::column(width = 6,shiny::numericInput("knotsPeriod", "KnotsPeriod",
rv$ptrset@parameter$knotsPeriod, 1, 10, 1)),
shiny::column(width = 10,shiny::selectInput(inputId = "methodKnot",
label = "Method for knot location ",
choices = c("Around expiration",
"Uniform"),
multiple = FALSE))
)
,
# delete des expirations et d'appliquer les changements de paramètres sur les expirations
shiny::fluidRow(
shiny::actionButton('reset', 'Apply for this file'),
shiny::actionButton('resetAll', 'Apply for all')),
shiny::p(class='text-center', shiny::actionButton('delete',
'Delete selected rows')
)
)
}
},quoted=FALSE)
# output$nomFile<-shiny::renderUI({
# if(!is.null(rv$ptrset && rv$new) ){
# shiny::fluidPage(
#
# #choose file in the ptrSet
# shiny::fluidRow(
# shiny::selectInput("fileName","File name:",as.list(names(rv$ptrset@TIC)),selectize=FALSE)
# ))
# }
# }
# )
#rv <- shiny::reactiveValues( data = NULL , bgPoints=NULL, ptrset= ptrSet )
# get the time limit of the selected file
#rv<-list()
shiny::observeEvent(input$fileName, {
if(!is.null(rv$ptrset)){
rv$data <- t(getTimeInfo(rv$ptrset)$timeLimit[[input$fileName]]$exp)
rv$bgPoints <- getTimeInfo(rv$ptrset)$timeLimit[[input$fileName]]$backGround
rv$knots<- getPeaksInfo(rv$ptrset)$knots[[input$fileName]]
rv$new <-FALSE
rv$newFile <-TRUE
}
})
#display time limit table
output$tableTimeLimit <- DT::renderDataTable( {
if(!is.null(rv$ptrset) & !is.null(input$fileName)){
#fileName<-input$fileNameTimeLimit
#indexTimeLimit <- rv$ptrset@timeLimit[[fileName]]$exp
DT::datatable(rv$data, editable = TRUE,
selection=list(target="row"),
rownames=as.character(seq(1,nrow(rv$data)))
)
}
})
### delete the selected expirations ----
shiny::observeEvent(input$delete, {
rowNum <- input$tableTimeLimit_rows_selected
if(length(rowNum) == nrow(rv$data)){
shiny::showNotification("At least one period must be selected",
duration = NULL, id="warnings" )
}else {
#shiny::removeNotification("warnings")
expirationTodelete<-rv$data[rowNum,,drop=FALSE]
knots<-rv$knots
knotTodelete<-Reduce(c,apply(expirationTodelete,1,
function(x) which(x[1] <= knots &
knots <= x[2])))
rv$data <- rv$data[-rowNum,,drop=FALSE]
rv$knots<-knots[-knotTodelete]
ptrSetTemp<-rv$ptrset
timeLimitInput<-getTimeInfo(ptrSetTemp)$timeLimit[[input$fileName]]
timeLimitInput$exp <- t(rv$data)
ptrSetTemp<-setTimeLimits(ptrSetTemp,newTimeLimites =timeLimitInput,index = input$fileName )
#ptrSetTemp<-setKnots(ptrSetTemp,rv$knots,input$fileName)
rv$ptrset<-ptrSetTemp
#ptrSetNew(ptrSet)
}
})
### reset the expirations with timeLimit function for the current file ----
shiny::observeEvent(input$reset, {
shiny::removeNotification("warnings")
fracMaxTICNew <- input$fracMaxTIC
##default value
fracMaxTICBgNew <- input$fracMaxTICBg
derivThresholdExpNew <- input$derivThresholdExp
derivThresholdBgNew <-input$derivThresholdBg
minPointsNew <-input$minPoints
degreeBaselineNew <- input$degreeBaseline
timeLimit<-timeLimitFun(TIC = getTimeInfo(rv$ptrset)$breathTracer[[input$fileName]],
fracMaxTIC =fracMaxTICNew ,
fracMaxTICBg = fracMaxTICBgNew,
derivThresholdExp = derivThresholdExpNew,
derivThresholdBg = derivThresholdBgNew,
minPoints =minPointsNew ,
degreeBaseline = degreeBaselineNew)
t<-as.numeric(names( getTimeInfo(rv$ptrset)$TIC[[input$fileName]]))
background<-timeLimit$backGround
if(input$methodKnot == "Around expiration")
method<-"expiration" else method<- "uniform"
knots<-try(defineKnotsFunc(t,background,input$knotsPeriod,method))
rv$data <- t(timeLimit$exp)
rv$bgPoints<- timeLimit$backGround
rv$knots<-knots
timeLimitInput<-getTimeInfo(rv$ptrset)$timeLimit[[input$fileName]]
timeLimitInput$exp <- t(rv$data)
timeLimitInput$backGround <- rv$bgPoints
rv$ptrset<-setTimeLimits(rv$ptrset,newTimeLimites =timeLimitInput,index = input$fileName )
rv$ptrset<-setKnots(rv$ptrset,rv$knots,input$fileName)
paramterTimeLimit<-list(fracMaxTIC=fracMaxTICNew,
fracMaxTICBg=fracMaxTICBgNew,
derivThresholdExp=derivThresholdExpNew,
derivThresholdBg=derivThresholdBgNew,
minPoints = minPointsNew,
degreeBaseline=degreeBaselineNew)
parameter<-getParameters(rv$ptrset)
parameter$knotsPeriod<-input$knotsPeriod
parameter$timeLimit<-paramterTimeLimit
rv$ptrset<- setParameters(rv$ptrset,parameter)
rv$new <-FALSE
rv$newFile <-FALSE
})
### reset the expirations with timeLimit function for all file ----
shiny::observeEvent(input$resetAll, {
#shiny::removeNotification("warnings")
fracMaxTICNew <- input$fracMaxTIC
##default value
fracMaxTICBgNew <- input$fracMaxTICBg
derivThresholdExpNew <- input$derivThresholdExp
derivThresholdBgNew <-input$derivThresholdBg
minPointsNew <-input$minPoints
degreeBaselineNew <- input$degreeBaseline
timeLimit<-lapply(names(getTimeInfo(rv$ptrset)$TIC),function(fileName) {
timeLimitFun(TIC = getTimeInfo(rv$ptrset)$breathTracer[[fileName]],
fracMaxTIC =fracMaxTICNew ,
fracMaxTICBg = fracMaxTICBgNew,
derivThresholdExp = derivThresholdExpNew,
derivThresholdBg = derivThresholdBgNew,
minPoints =minPointsNew ,degreeBaseline = degreeBaselineNew)
})
names(timeLimit) <- names(getTimeInfo(rv$ptrset)$TIC)
knots<-lapply(names(getTimeInfo(rv$ptrset)$timeLimit),function(fileName) {
background<-timeLimit[[fileName]]$backGround
t<-as.numeric(names( getTimeInfo(rv$ptrset)$TIC[[fileName]]))
if(input$methodKnot == "Around expiration") {
defineKnotsExpiration(t,background,input$knotsPeriod)
} else {
unique(c(t[1],
seq(t[1],utils::tail(t,1),by=input$knotsPeriod),
utils::tail(t,1)))
}
})
names(knots)<-names(timeLimit)
rv$data <- t(timeLimit[[input$fileName]]$exp)
rv$bgPoints<- timeLimit[[input$fileName]]$backGround
rv$knots<-knots[[input$fileName]]
rv$ptrset<-setTimeLimits(rv$ptrset,timeLimit)
rv$ptrset<-setKnots(rv$ptrset,knots)
paramterTimeLimit<-list(fracMaxTIC=fracMaxTICNew,
fracMaxTICBg=fracMaxTICBgNew,
derivThresholdExp=derivThresholdExpNew,
derivThresholdBg=derivThresholdBgNew,
minPoints = minPointsNew,
degreeBaseline=degreeBaselineNew)
parameter<-getParameters(rv$ptrset)
parameter$knotsPeriod<-input$knotsPeriod
parameter$timeLimit<-paramterTimeLimit
rv$ptrset<- setParameters(rv$ptrset,parameter)
})
# display the expirations in data table ----
output$table <- DT::renderDataTable( {
if(!is.null(rv$data))
#shiny::removeNotification("warnings")
DT::datatable(rv$data, editable = TRUE,
selection=list(target="row"),
rownames=as.character(seq(1,nrow(rv$data)))
)
})
shiny::observeEvent(input$tableTimeLimit_cell_edit,
{
rv$data[ input$tableTimeLimit_cell_edit$row ,
input$tableTimeLimit_cell_edit$col] <- as.numeric(input$tableTimeLimit_cell_edit$value)
timeLimitInput<-getTimeInfo(rv$ptrset)$timeLimit[[input$fileName]]
timeLimitInput$exp <- t(rv$data)
rv$ptrset<-setTimeLimits(rv$ptrset,newTimeLimites =timeLimitInput,index = input$fileName )
}
)
# PlotTimeLimit ----
output$plotTimeLimit <- plotly::renderPlotly({
if(!is.null(rv$ptrset) & !is.null(input$fileName) & !is.null(rv$data)){
s <- input$tableTimeLimit_rows_selected
fileName <- input$fileName
TIC <- getTimeInfo(rv$ptrset)$breathTracer[[fileName]]
time <- as.numeric(names(TIC))
indexTimeLimit <- t(rv$data)
#indexTimeLimit <- rv$ptrset@timeLimit[[fileName]]$exp
expPoint<-Reduce(c,apply(indexTimeLimit,2,function(x) seq(x[1],x[2])))
bgPoint<-rv$bgPoints
#bgPoint<-rv$ptrset@timeLimit[[fileName]]$backGround
knots<-rv$knots
p <- ggplot2::qplot(x=time,y=TIC,
xlab="time",ylab="intensity",
main=paste("Trace of",input$fileName))
if(!is.null(expPoint))
p<-p+ggplot2::geom_point(mapping=ggplot2::aes(time ,y,colour=point),
data=data.frame(time= time[expPoint],y=TIC[expPoint],point="exp"))
if(!is.null(bgPoint))
p<-p + ggplot2::geom_point(mapping=ggplot2::aes(time ,y,colour=point),
data=data.frame(time= time[bgPoint],y=TIC[bgPoint],point="Background"))
p <- p + ggplot2::theme_classic()
if(!is.null(knots)){
p<- p + ggplot2::geom_point(mapping=ggplot2::aes(time ,y,colour=point),
data=data.frame(time= knots,
y=rep(0,length(knots)),
point="knots"),shape=4) +
ggplot2::ggtitle(paste("Trace of",input$fileName,length(knots)))
}
if( length(s) ){
s <- s[s<=ncol(indexTimeLimit)] #to avoid warnings
expirationSelect<-Reduce(c,apply(indexTimeLimit[,s,drop=FALSE],2,function(x) seq(x[1],x[2])))
if(length(s)) p <- p +
ggplot2::geom_point(mapping=ggplot2::aes(time ,y,colour=point),
data=data.frame(time= time[expirationSelect],
y=TIC[expirationSelect],
point="Expiration selected"))
p<- p + ggplot2::scale_colour_manual(values = c("#F8766D","#7CAE00",
"#C77CFF","#00BFC4"))
}
plotly::ggplotly(p)
}
})
# Calibration ----
output$paramCalib<- shiny::renderUI({
if(!is.null(rv$ptrset)){
shiny::fluidPage(
shiny::fluidRow(
shiny::selectInput("fileNameCalib","File name:",as.list(names(rv$ptrset@TIC)),selectize=FALSE),
shiny::fluidRow(shiny::h4("Calibration masses"),
shiny::h6("To remove a mass, put its value to 0. At least two masses are required") ),
),
# shiny::fluidRow(shiny::h5(strong(length(rv$ptrset@parameter$mzCalibRef)))),
# shiny::fluidRow(shiny::h4("Calibration masses"),
#
# shiny::column(4,shiny::numericInput(inputId = "mz1New",label = "mz1",value = rv$ptrset@parameter$mzCalibRef[1])),
# shiny::column(4,shiny::numericInput(inputId = "mz2New",label = "mz2",value =rv$ptrset@parameter$mzCalibRef[2])),
# shiny::column(4,shiny::numericInput(inputId = "mz3New",label = "mz3",value = rv$ptrset@parameter$mzCalibRef[3])),
# shiny::column(4,shiny::numericInput(inputId = "mz4New",label = "mz4",value = rv$ptrset@parameter$mzCalibRef[4]))
# ),
)
}
})
output$paramCalib2<- shiny::renderUI({
if(!is.null(rv$ptrset)){
lapply(1:length(rv$ptrset@parameter$mzCalibRef), function(i) {
output[[paste0('b', i)]] <- shiny::renderUI({
shiny::fluidRow(
#Affichage des nouvelles masses
shiny::numericInput(inputId = paste0("mz", i,"New"), label = paste("mz", i), value = rv$ptrset@parameter$mzCalibRef[i]),
# #Boutons pour effacer les masses
# shiny::actionButton(inputId = paste0("close", i),label="X")
)
})
})
}
})
output$paramCalib3<- shiny::renderUI({
if(!is.null(rv$ptrset)){
shiny::fluidPage(
shiny::fluidRow(
shiny::p(class='text-center',
shiny::actionButton("resetCalib",label = "Reset calibration"))
)
# shiny::fluidRow(
# shiny::p(class='text-center',
# shiny::actionButton("addCalib",label = "Add calibration"))
# )
)
}
})
output$paramCalib4 <- shiny::renderUI({
if(!is.null(rv$ptrset)){
shiny::fluidPage(
shiny::fluidRow(
shiny::p(class='text-center',
shiny::actionButton("addMassButton","Add mass"))
)
)
}
})
# masse <- eventReactive(input$addMassButton,{
# if(!is.null(rv$ptrset)){
# #shiny::numericInput(inputId = "IdAddedMass", label = paste("mz", length(rv$ptrset@parameter$mzCalibRef)+1), value = 60)
# #print(input$IdAddedMass)
# #rv$ptrset@parameter$mzCalibRef[[length(rv$ptrset@parameter$mzCalibRef)+1]] <- input$IdAddedMass
# rv$ptrset@parameter$mzCalibRef[[length(rv$ptrset@parameter$mzCalibRef)+1]] <- 0
#
# }
# })
#
# output$addMass_UI <- renderUI({
# masse()
# })
# Reset Calib
shiny::observeEvent(input$resetCalib,{
mzCalibRef = c()
for (i in 1:length(rv$ptrset@parameter$mzCalibRef)){
if (eval(parse(text=paste0("input$mz",i,"New!=0")))){
mzCalibRef <-c(mzCalibRef,eval(parse(text=paste0("input$mz",i,"New"))))
}
}
rv$ptrset<-calibration(rv$ptrset,mzCalibRef)
})
# Add Mass initialisée à 0
shiny::observeEvent(input$addMassButton,{
rv$ptrset@parameter$mzCalibRef[length(rv$ptrset@parameter$mzCalibRef)+1] <- 0
})
# shiny::observeEvent( function(i){
#
#
# input$closei
# {
# rv$ptrset@parameter$mzCalibRef <- rv$ptrset@parameter$mzCalibRef[-length(rv$ptrset@parameter$mzCalibRef)]
# }
# }
# )
# # Close mass
# shiny::observeEvent( input$close3, {
# print(length(rv$ptrset@parameter$mzCalibRef))
# rv$ptrset@parameter$mzCalibRef <- rv$ptrset@parameter$mzCalibRef[-3]
#
# }
#
# )
output$plotCalib<- shiny::renderPlot({
if(!is.null(rv$ptrset)) plotCalib(rv$ptrset,file=input$fileNameCalib)
})
# shiny::observeEvent(input$close, {
# shiny::stopApp(ptrSet)
# })
#
# Détection des pics ----
shiny::observeEvent(input$detectPeak, {
ptrSet<-rv$ptrset
resolution<-c(as.numeric(input$resMin),
as.numeric(input$resMean),
as.numeric(input$resMax))
rv$ptrset<-detectPeak(rv$ptrset,ppm = as.numeric(input$PPM),
minIntensity =as.numeric(input$minIntensity) ,
resolutionRange =NULL )
rv$ptrset<-rv$ptrset
})
## Choix du fichier ----
output$secondSelectionFileRawData<-shiny::renderUI({
if(!is.null(rv$ptrset)){
shiny::fluidPage( shiny::selectInput(inputId = "plotRaw",label = "File to plot",
choices= c(names(rv$ptrset@peakList)),
selectize=FALSE)
)
}
})
# Choix du feature ----
output$secondSelectionMzRawData<-shiny::renderUI({
if(!is.null(rv$ptrset) & !is.null(input$plotRaw)){
shiny::fluidPage( shiny::selectInput(inputId = "plotRawmz",label = "features",
choices= c(rownames(Biobase::exprs(rv$ptrset@peakList[[input$plotRaw]]))),
selectize=FALSE)
)
}
})
# Plot de détection de peaks ----
output$RawData<-shiny::renderPlot({
if(!is.null(rv$ptrset)){
if(!is.null(input$plotRawmz)){
peakList<-Biobase::fData(getPeakList(rv$ptrset)[[input$plotRaw]])
peaksParam <- peakList[as.character(input$plotRawmz),
c("Mz","parameterPeak.delta1",
"parameterPeak.delta2",
"parameterPeak.height")]
fctFit <- rv$ptrset@fctFit[[input$plotRaw]]
peakShape<-rv$ptrset@peakShape[[input$plotRaw]]
peaks <- function(mz) eval(parse(text = paste0("ptairMS:::",fctFit)))(peaksParam[1,"Mz"],
peaksParam[1,"parameterPeak.delta1"],
peaksParam[1,"parameterPeak.delta2" ],
peaksParam[1,"parameterPeak.height"],
mz,
peakShape)
temporalEstim<- Biobase::exprs(getPeakList(rv$ptrset)[[input$plotRaw]])[as.character(input$plotRawmz),]
fileFullName<- getFileNames(rv$ptrset,fullNames =TRUE )[ getFileNames(rv$ptrset)==input$plotRaw]
g<-plotPeakRaw(set = rv$ptrset,mzRange = as.numeric(input$plotRawmz),
file=fileFullName,peaks = peaks,fctFit=fctFit,temporalEstim = temporalEstim,
ppm = 700)
print(g)
}
}
})
output$group <-shiny::renderUI({
if(!is.null(rv$ptrset)){
shiny::fluidPage(shiny::selectInput(inputId = "group",label = "Select group",
choices= c("NULL",colnames(rv$ptrset@sampleMetadata)),
selectize=FALSE))
}
})
#
shiny::observeEvent(input$align, {
ptrSet<-rv$ptrset
pValThres<-input$pValThres
group<-NULL
if(input$group!="NULL") group<-input$group
eSet<- ptairMS::alignSamples(ptrSet,ppmGroup = 90,fracGroup = 1- input$fracGroup ,group = group,
pValGreaterThres = pValThres,pValLessThres = pValThres,
fracExp = input$fracExp,quantiUnit=input$quantiUnit)
rv$eset<-eSet
})
output$nbPeak <- shiny::renderText({
if(!is.null( rv$eset)){
X<-Biobase::exprs(rv$eset)
paste(nrow(X),"peaks aligned")
}
})
output$tableAlign<- plotly::renderPlotly({
if(!is.null( rv$eset)){
X<-Biobase::exprs(rv$eset)
if(input$Transformation == "log2"){
X<-log2(X)
} else if (input$Transformation == "Centred reduced"){
X<-t(apply(X,1,function(x) (x-mean(x,na.rm=TRUE))/sd(x,na.rm=TRUE)))
}
Y<-Biobase::pData(rv$eset)
#ropls::imageF(log2(Biobase::exprs(rv$eset)))
plotly::plot_ly(z = X,
x = substr(colnames(Biobase::exprs(rv$eset)),1,7),
y = paste0("mz-",as.character(rownames(Biobase::exprs(rv$eset)))),
type = "heatmap", colorscale='Jet')
}
})
shiny::observeEvent(input$impute,{
if(!is.null(rv$eset) & !is.null(rv$ptrset)){
rv$eset <- impute(eSet = rv$eset,ptrSet = rv$ptrset,parallelize = FALSE)
}
})
output$secondSelectionLongitudinal<-shiny::renderUI({
if(!is.null(rv$ptrset) & !is.null(rv$eset)){
shiny::fluidPage(
shiny::selectInput("mzLongotudinal","Feature",
rownames(Biobase::exprs(rv$eset)),
selectize=FALSE),
shiny::selectInput("idPatient","idPatient",
c("None",colnames(rv$ptrset@sampleMetadata)),
selectize=FALSE),
shiny::selectInput("timeColumn","x-axis",
c("None",colnames(rv$ptrset@sampleMetadata)),
selectize=FALSE),
shiny::selectInput("columnLongitudinal","Colored by:",
c("None",colnames(rv$ptrset@sampleMetadata)),
selectize=FALSE) )
}
})
output$dataLongitudinal<-plotly::renderPlotly({
if(!is.null(rv$eset) ){
if(!is.null(input$timeColumn) & !is.null(input$columnLongitudinal)){
if(input$timeColumn != "None" & input$columnLongitudinal != "None"){
X<-Biobase::exprs(rv$eset)
Y<-Biobase::pData(rv$eset)
mz<-input$mzLongotudinal
colTime<-input$timeColumn
colorby<-input$columnLongitudinal
name<-input$idPatient
Y$file<-rownames(Y)
quanti<-Biobase::annotation(rv$eset)
g <- ggplot2::ggplot()
for(j in unique(Y[,name])){
if(all(!is.na(Y[Y[,name] == j,colTime]))){
g <- g+ suppressWarnings(ggplot2::geom_line(ggplot2::aes(x=timeC,y=cps,color=filter,label=files,group=name),
data=data.frame(timeC =Y[Y[,name] == j,colTime],
cps=X[as.character(mz),Y[,name]==j],
filter=Y[Y[,name] == j,colorby],
files=rownames(Y)[Y[,name] == j],
name=j))) +
suppressWarnings(ggplot2::geom_point(ggplot2::aes(x=timeC,y=cps,color=filter,label=files),
data=data.frame(timeC=Y[Y[,name] == j,colTime],
cps=X[as.character(mz),Y[,name]==j],
filter=Y[Y[,name] == j,colorby],
files=rownames(Y)[Y[,name] == j],
name=j)))
}
}
g<-g + ggplot2::ggtitle(mz,annotateVOC(as.numeric(mz),ppm=100)[3]) +
ggplot2::labs(y= quanti, x = colTime )
`%>%` <- plotly::`%>%`
plotly::ggplotly(g) %>%
plotly::layout(title = list(text = paste0(mz,
'<br>',
'<sup>',
annotateVOC(as.numeric(mz),ppm=100)[3],
'</sup>')))
}
}
}
})
output$pca<-shiny::renderUI({
if(!is.null(rv$ptrset)){
shiny::fluidPage(
shiny::selectInput("colorPca","Colored by:",
colnames(rv$ptrset@sampleMetadata),
selectize=FALSE)
)
}
})
output$pcaMarker<-shiny::renderUI({
if(!is.null(rv$ptrset)){
shiny::fluidPage(
shiny::selectInput("markerPca","Marker:",
c("sampleNames",colnames(rv$ptrset@sampleMetadata)),
selectize=FALSE)
)
}
})
#plot acps
output$acp <- plotly::renderPlotly({
if(!is.null(rv$eset) & !is.null(input$markerPca) ){
# getting Shiny parameters
eset <- rv$eset
# log2 transformation
X<-Biobase::exprs(eset)
X[X<0]<-min(X[X>0],na.rm=FALSE)
Biobase::exprs(eset) <- log2(X)
set.pca <- ropls::opls(eset, predI = 2, info.txtC = "none", fig.pdfC = "none",
crossvalI =4)
rv$pca<-set.pca
if( !is.na(input$x) & !is.na(input$y)){
if(input$x !=input$y){
score_plotly(set.pca,
components.vi = c(input$x, input$y),
label.c = input$markerPca,
color.c = input$colorPca,
ellipse.l = FALSE,
palette.c = "",
#info.vc = c("sampleNames",color),
size.ls = list(legend_title.i = 8,
legend_text.i = 8))
}
}
}
})
output$getLoading<-shiny::renderTable({
if(!is.null(rv$pca)){
X<-Biobase::exprs(rv$eset)
importance<-ropls::getLoadingMN(rv$pca)
tx<-rownames(X)[order(importance[,input$x]^2,decreasing = TRUE)[seq_len(input$maxRow)]]
ty<-rownames(X)[order(importance[,input$y]^2,decreasing = TRUE)[seq_len(input$maxRow)]]
data<-cbind(mz.tx=tx,annotation.tx=ptairMS::annotateVOC(as.numeric(tx))[,3],
mz.ty=ty,annotation.ty=ptairMS::annotateVOC(as.numeric(ty))[,3])
colnames(data)<-gsub(pattern = "x",replacement = input$x,x = colnames(data) )
colnames(data)<-gsub(pattern = "y",replacement = input$y,x = colnames(data) )
data
}
})
}
shiny::shinyApp(ui = ui, server = server)
}
camilleroquencourt/ptairMS documentation built on April 24, 2024, 9:03 p.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.
Defines functions RunShinnyApp score_plotly plotPeakRaw
Documented in RunShinnyApp
utils::globalVariables(c("time", "intensity", "sd", "filter","cps","x","z",
"intensities","timeC","files"))
plotPeakRaw<-function(set,file, mzRange, peaks, temporalEstim,fctFit,
ppm = 2000,
palette = c("heat")[1]) {
if (length(mzRange) == 1)
mzRange <- mzRange + c(-1, 1) * mzRange * ppm * 1e-06
mz <- rhdf5::h5read(file, name = "FullSpectra/MassAxis")
mzRange[1] <- max(min(mz), mzRange[1], na.rm = TRUE)
mzRange[2] <- min(max(mz), mzRange[2], na.rm = TRUE)
# get the index of the aroud mzRange
index <- which(mzRange[1] < mz & mz < mzRange[2])
# object data
object <- rhdf5::h5read(file, name = "/FullSpectra/TofData",
index = list(index, NULL, NULL, NULL))
# time axis
timeVn <- as.numeric(names(getTimeInfo(set)$TIC[[basename(file)]]))
# calibrate mass axis
FirstcalibCoef <- try(rhdf5::h5read(file, "FullSpectra/MassCalibration",
index = list(NULL,1)))
attributCalib <- try(rhdf5::h5readAttributes(file, "/FullSpectra"))
if (!is.null(attr(FirstcalibCoef, "condition")) & is.null(attr(attributCalib, "condition"))) {
FirstcalibCoef <- matrix(c(attributCalib$`MassCalibration a`, attributCalib$`MassCalibration b`),
ncol = 1)
}
tof <- sqrt(mz) * FirstcalibCoef[1, 1] + FirstcalibCoef[2, 1]
# tof<- seq(0,length(mz))
coefCalib <- getCalibrationInfo(set)$coefCalib[[basename(file)]][[1]]
mzVn <- ((tof - coefCalib["b", ])/coefCalib["a", ])^2
mzVn <- mzVn[index]
# formate object matix
rawSubMN <- matrix(object, nrow = dim(object)[1],
ncol = prod(utils::tail(dim(object), 2)))
rawSubMN <- rawSubMN[,seq_len(length(timeVn)),drop=FALSE]
imageMN<-rawSubMN
dimnames(imageMN) <- list(mzVn, timeVn)
## chr: Current
bin<-diff(timeVn)[1]
chromVn <- apply(rawSubMN, 2, function(intVn) sum(intVn, na.rm = TRUE)/bin )
temporal <- ggplot2::ggplot() +
ggplot2::geom_point(data=data.frame(time=timeVn,cps=chromVn),
mapping = ggplot2::aes(x=time,y=cps)) + ggplot2::theme_classic()
temporal<-temporal + ggplot2::geom_line(data=data.frame(time=timeVn,cps=temporalEstim),
mapping = ggplot2::aes(x=time,y=cps))
## sca: Color scale
df <- data.frame(x = 1, y = seq_len(236), z = seq_len(236))
sca <- ggplot2::ggplot(df, ggplot2::aes(x, y)) +
ggplot2::geom_tile(ggplot2::aes(fill = z), size = 5) +
ggplot2::labs(x = NULL, y = NULL)+
ggplot2::scale_x_continuous(expand = c(0, 0)) +
ggplot2::scale_y_continuous(expand = c(0, 0))+
ggplot2::scale_fill_gradientn(colours = rev(grDevices::rainbow(100, end = 4/6)))
## ima: Image
rawM<-ggplot2::ggplot()
data<-data.frame(time=rep(timeVn,each=nrow(imageMN)),
mz=rep(as.numeric(rownames(imageMN)),ncol(imageMN)),
intensity=c(imageMN))
rawM <- ggplot2::ggplot() +
ggplot2::geom_tile(data=data, mapping=ggplot2::aes(time, mz, fill= intensity),show.legend =FALSE) +
ggplot2::scale_fill_gradientn(colours = rev(grDevices::rainbow(100, end = 4/6)))+
ggplot2::theme_classic()+
ggplot2::scale_x_continuous(expand = c(0, 0)) +
ggplot2::scale_y_continuous(expand = c(0, 0))+
ggplot2::theme(plot.title = ggplot2::element_blank(),
axis.title.x = ggplot2::element_text(size =12 ),
axis.title.y = ggplot2::element_text(size = 12),
axis.text = ggplot2::element_text(size = 10),
legend.title = ggplot2::element_text(size = 12),
legend.text = ggplot2::element_text( size = 10),
plot.caption = ggplot2::element_text(hjust = 0.5,size = 13) )
## spe: Spectrum
timeiNTER<-diff(timeVn)[1]
specVn <- apply(rawSubMN, 1, function(intVn) mean(intVn, na.rm = TRUE))
spctr<- ggplot2::ggplot()+
ggplot2::geom_point(data=data.frame(mz=as.numeric(rownames(imageMN)),intensities=specVn),
mapping = ggplot2::aes(x=mz,y=intensities)) + ggplot2::theme_classic()+
ggplot2::coord_flip()
spctr<- spctr + ggplot2::geom_line(data=data.frame(mz=as.numeric(rownames(imageMN)),
y=peaks( as.numeric(rownames(imageMN)) )),
mapping=ggplot2::aes(x=mz,y=y))
(ggpubr::ggarrange(
ggpubr::ggarrange(temporal,rawM,nrow=2,ncol=1,align = "v",heights=c(0.25,0.75)),
ggpubr::ggarrange(sca,spctr,nrow=2,ncol=1,heights=c(0.25,0.75)),
widths=c(0.75,0.25),ncol=2,nrow=1))
}
score_plotly <- function(ropls.model,label.c = "sampleNames",color.c = "",info.vc = "all",
title.c = "", components.vi = c(1, 2),palette.c = "Set1",ellipse.l = TRUE,
size.ls = list(axis_lab.i = 16,
axis_text.i = 14,
point.i = 3,
label.i = 5,
title.i = 20,
legend_title.i = 15,
legend_text.i = 15),
figure.c = c("interactive",
"interactive_plotly",
"my_scoreplot.pdf",
"my_scoreplot.html")[2])
{
# checking arguments and preparing data ----
## dataset [ExpressionSet] ----
eset <- ropls::getEset(ropls.model)
if (any(dim(eset) < 1))
stop("ExpressionSet object could not be extracted from the 'ropls.model'")
pdata.df <- Biobase::pData(eset)
#pdata.df$date<-as.factor(pdata.df$date)
data.df <- cbind.data.frame(sampleNames = Biobase::sampleNames(eset),
pdata.df,
stringsAsFactors = FALSE)
## plotly info ----
if (length(info.vc) == 1 && info.vc == "all") {
text.df <- data.df
} else {
info_in_metadata.vl <- info.vc %in% colnames(data.df)
if (any(!info_in_metadata.vl)) {
if (all(!info_in_metadata.vl)) {
stop("None of the selected info.vc names was found in the sampleMetadata:\n",
paste(info.vc, collapse = ", "))
} else {
warning("The following columns were not found in the sampleMetadata:\n",
paste(info.vc[!info_in_metadata.vl], collapse = ", "))
}
}
text.df <- data.df[, info.vc[info_in_metadata.vl], drop = FALSE]
}
text.vc <- apply(text.df, 1,
function(row.vc)
paste(paste0(colnames(text.df), " = ", row.vc), collapse = "\n"))
## score vectors ----
score.mn <- ropls::getScoreMN(ropls.model)
data.df <- cbind.data.frame(data.df,
text = text.vc,
score.mn)
## labels ----
#stopifnot(length(label.c) == 1)
if (label.c != "")
stopifnot(label.c %in% colnames(data.df))
## colors ----
#stopifnot(length(color.c) == 1)
if (color.c != "") {
stopifnot(color.c %in% colnames(data.df))
if (is.factor(data.df[, color.c]) || is.character(data.df[, color.c])) {
color_type.c <- "qualitative"
} else
color_type.c <- "quantitative"
}
## components ----
stopifnot(length(components.vi) == 2)
stopifnot(max(components.vi) <= ncol(score.mn))
## sizes ----
size_default.vi <- c(axis_lab.i = 16,
axis_text.i = 14,
point.i = 3,
label.i = 5,
title.i = 20,
legend_title.i = 15,
legend_text.i = 15)
for (size.c in names(size_default.vi)) {
if (!(size.c %in% names(size.ls)))
size.ls[[size.c]] <- size_default.vi[size.c]
}
## filename extention
filename_ext.c <- utils::tail(unlist(strsplit(basename(figure.c), ".", fixed = TRUE)), 1)
# starting the plot [ggplot]
p <- eval(parse(text = paste0("ggplot2::ggplot(data.df, ggplot2::aes(x = ",
paste0('p', components.vi[1]),
", y = ",
paste0('p', components.vi[2]),
ifelse(color.c != "",
paste0(", color = ", color.c),
""),
ifelse(label.c != "",
paste0(", label = ", label.c),
""),
", text = text))")))
## text/points [geom_text/geom_point] ----
if (label.c != "") {
p <- p + ggplot2::geom_text(size = size.ls[["label.i"]], ggplot2::aes(fontface = "bold"))
} else {
p <- p + ggplot2::geom_point(size = size.ls[["point.i"]])
}
## horizontal and vertical lines [geom_hline, geom_vline] ----
p <- p + ggplot2::geom_hline(ggplot2::aes(yintercept = 0)) +
ggplot2::geom_vline(ggplot2::aes(xintercept = 0))
## ellipses [stat_ellipse] ----
p <- p + eval(parse(text = paste0("ggplot2::stat_ellipse(ggplot2::aes(x = ",
paste0('p', components.vi[1]),
", y = ",
paste0('p', components.vi[2]),
", group = 1), type = 'norm')")))
if (ellipse.l && color.c != "" && color_type.c == "qualitative")
p <- p + eval(parse(text = paste0("ggplot2::stat_ellipse(ggplot2::aes(x = ",
paste0('p', components.vi[1]),
", y = ",
paste0('p', components.vi[2]),
", group = ",
ifelse(color.c != "", color.c, 1),
"), type = 'norm')")))
# title and axis labels [labs]
p <- p + ggplot2::labs(title = title.c,
x = paste0("t", components.vi[1],
" (",
round(ropls.model@modelDF[components.vi[1], "R2X"] * 100),
"%)"),
y = paste0("t", components.vi[2],
" (",
round(ropls.model@modelDF[components.vi[2], "R2X"] * 100),
"%)"))
# theme [them_bw, theme]
p <- p + ggplot2::theme_bw() +
ggplot2::theme(plot.title = ggplot2::element_text(size = size.ls[["title.i"]], face = "bold"),
axis.title.x = ggplot2::element_text(size = size.ls[["axis_lab.i"]], face = "bold"),
axis.title.y = ggplot2::element_text(size = size.ls[["axis_lab.i"]], face = "bold"),
axis.text = ggplot2::element_text(size = size.ls[["axis_text.i"]]),
legend.title = ggplot2::element_text(face = "bold", size = size.ls[["legend_title.i"]]),
legend.text = ggplot2::element_text(face = "bold", size = size.ls[["legend_text.i"]]))
# palette [scale_colour_brewer, scale_colour_gradientn]
if (color.c != "") {
if (color_type.c == "qualitative") {
if (palette.c != "")
p <- p + ggplot2::scale_colour_brewer(palette = palette.c)
} else
p <- p + ggplot2::scale_colour_gradientn(colours = rev(grDevices::rainbow(100, end = 4/6)))
}
# display/saving [plotly::ggplotly, plotly::layout, htmlwidgets::saveWidget, plotly::as_widget]
if (figure.c == "interactive_plotly" || filename_ext.c == "html") {
p <- plotly::ggplotly(p, tooltip = "text")
p <- plotly::layout(p, hoverlabel = list(font = list(size = 20)))
if (filename_ext.c == "html") {
#htmlwidgets::saveWidget(plotly::as_widget(p), figure.c)
return(p)
} else {
#print(p)
return(p)
}
} else {
if (filename_ext.c == "pdf")
grDevices::pdf(figure.c)
#print(p)
if (filename_ext.c == "pdf")
grDevices::dev.off()
return(p)
}
}
################# ui -----
#' Graphical interface of ptairMS workflow
#'
#' The whole workflow of ptairMS can be run interactively through a graphical user interface,
#' which provides visualizations (expiration phases, peaks in the raw data, peak table, individual VOCs),
#' quality controls (calibration, resolution, peak shape and evolution of reagent ions depending on time),
#' and exploratory data analysis.
#' @return Shinny app
#' @examples
#' \dontrun{RunShinnyApp()}
#' @rdname RunShinnyApp
#' @export
RunShinnyApp<-function(){
#' @importFrom shinyscreenshot screenshotButton
ui <- shiny::navbarPage("ptairMS",
# Application title
#titlePanel("ptairMS"),
#tabsetPanel(type = "tabs",
shiny::tabPanel("Read and check data",
shiny::fluidPage(
shiny::h3("Create/Load a PtrSet a from directory"),
shiny::selectInput("createOrLoad", "Choose action", c("loadPtrSet","createPtrSet"),
multiple=FALSE),
shiny::uiOutput("param")
),
##UI Affichage du Ptrset ----
shiny::sidebarLayout(
shiny::sidebarPanel(
shiny::h3("Your PtrSet:"),
shiny::verbatimTextOutput("showPtrSet",placeholder = FALSE),
shiny::uiOutput("update")
),
##UI tracé du PtrSet ----
shiny::mainPanel(
shiny::plotOutput("plotPtrSet"))),
##UI Calibration ----
shiny::sidebarLayout(
shiny::sidebarPanel(
shiny::h3("Calibration"),
shiny::uiOutput("paramCalib"),
shiny::uiOutput("paramCalib2"),
shiny::uiOutput("paramCalib3"),
shiny::uiOutput("paramCalib4"),
shiny::uiOutput("addMass_UI"),
# shiny::uiOutput("addMass")
),
shiny::mainPanel(
shiny::plotOutput("plotCalib"))),
shiny::sidebarLayout(
shiny::sidebarPanel(
shiny::h3("Expirations phases"),
# shiny::uiOutput("nomFile"),
shiny::uiOutput("paramTimeLimit")
),
shiny::mainPanel(
shiny::splitLayout(
DT::dataTableOutput("tableTimeLimit"),
plotly::plotlyOutput("plotTimeLimit")
))
),
shiny::fluidPage(
shinyscreenshot::screenshotButton()
)
),
shiny::tabPanel("Detect peak",
shiny::fluidRow(shiny::h3("Detect peak")),
shiny::fluidRow(
shiny::column( shiny::numericInput("PPM","min ppm sepration",130,0,200,10),width = 3),
shiny::column(shiny::numericInput("minIntensity","min intensity (cps)",5,0,200,10),width = 3),
shiny::column(shiny::numericInput("resMin ","resolution min",2000,0,20000,1000),width = 3),
shiny::column(shiny::numericInput("resMean ","resolution mean",5000,0,20000,1000),width = 3),
shiny::column(shiny::numericInput("resMax","resolution max",10000,0,20000,1000),width = 3)
),
shiny::fluidRow(
shiny::column( shiny::actionButton("detectPeak", "Detect peaks"),align="center",width = 12)
),
shiny::sidebarLayout(
shiny::sidebarPanel(
shiny::h3("Single file visualization"),
shiny::uiOutput("secondSelectionFileRawData"),
shiny::uiOutput("secondSelectionMzRawData")
),
#Plot
shiny::mainPanel(shiny::plotOutput("RawData"))
),
shiny::fluidPage(
shinyscreenshot::screenshotButton()
)
),
shiny::tabPanel("Align samples",
# alignement
# alignement
shiny::sidebarLayout(
shiny::sidebarPanel(
shiny::fluidPage(
shiny::h3("Alignment between samples"),
shiny::selectInput("quantiUnit","Unit:", c("ppb", "ncps", "cps"),selectize=FALSE),
shiny::numericInput("fracGroup","Maximum percentage of missing values per features",value = 0.3,min = 0,max = 1,step = 0.1),
shiny::uiOutput("group"),
shiny::numericInput("fracExp",
"Minimum percentage of samples such that features should be significativly
diffrent from ambiant air:",value = 0.1,min = 0,max = 1,step = 0.1),
shiny::numericInput("pValThres",
"The minimum p-value of the test between ambiant air and expirations:",value = 0.005,min = 0,max = 1,step = 0.1),
shiny::fluidRow(
shiny::column(width = 4, shiny::actionButton('align', 'Align samples')),
shiny::column(width = 4,shiny::verbatimTextOutput("nbPeak",placeholder = TRUE)),
shiny::column(width = 4,shiny::actionButton('export',"Export"))),
shiny::selectInput("Transformation","Matrix transformation:",c("log2","Centred reduced","None"),
selected = FALSE),
shiny::fluidRow(
shiny::column(width = 6, shiny::actionButton("impute", label = "Impute")),
shiny::column(width = 6,shiny::actionButton("outlier","Delete outlier")))
), width = 5),
# Show a plot of the generated distribution
shiny::mainPanel( plotly::plotlyOutput("tableAlign"), width = 7)),
shiny::sidebarLayout(
shiny::sidebarPanel(
shiny::h3("Metadata"),
shiny::uiOutput("secondSelectionLongitudinal")
),
# Show a plot of the generated distribution
shiny::mainPanel(plotly::plotlyOutput("dataLongitudinal"))
),
shiny::fluidPage(
shinyscreenshot::screenshotButton()
)
),
shiny::tabPanel("Statistical analysis",
shiny::fluidRow(
shiny::sidebarPanel(
shiny::h3("Principal Component Analysis"),
shiny::numericInput("x","Principal component of x-axis",1,1,4,1),
shiny::numericInput("y","Principal component of y-axis",2,1,4,1),
shiny::uiOutput("pca"),
shiny::uiOutput("pcaMarker")
),
# Show a plot of the generated distribution
shiny::mainPanel( plotly::plotlyOutput("acp"))
),
shiny::fluidRow(
shiny::sidebarPanel(
shiny::h3("Loading: features order by contribution"),
shiny::numericInput("maxRow","Number of row to display",10,1,100,1)
),
shiny::mainPanel(shiny::tableOutput("getLoading"))
),
shiny::fluidPage(
shinyscreenshot::screenshotButton()
)
)
#)
)
# Define server logic required to draw a histogram ----
server <- function(input, output) {
paramRv<-shiny::reactiveValues(path=NULL)
rv <- shiny::reactiveValues(ptrset=NULL, data=NULL,bgPoints=NULL,new=FALSE,file=NULL,newFile=TRUE)
## UI création d'un PtrSet ----
output$param<- shiny::renderUI({
if(input$createOrLoad == "createPtrSet"){
rv$new=TRUE
shiny::fluidPage(
shiny::fluidRow(
shiny::column(3,shiny::actionButton("selectDir","Select a directory")),
shiny::column(6,shiny::verbatimTextOutput(outputId = "showDirectorySelect",
placeholder = TRUE)),
shiny::column(3,shiny::textInput(inputId = "ptrName",label = "set name"))),
shiny::fluidRow(shiny::h4("Calibration masses"),
shiny::column(4,shiny::numericInput(inputId = "mz1",label = "mz1",value = 21.022)),
shiny::column(4,shiny::numericInput(inputId = "mz2",label = "mz2",value = 29.013424)),
shiny::column(4,shiny::numericInput(inputId = "mz3",label = "mz3",value = 60.0525)),
shiny::column(4,shiny::numericInput(inputId = "mz4",label = "mz4",value = 203.943)),
shiny::column(4,shiny::numericInput(inputId = "mz5",label = "mz5",value = 330.8495))),
shiny::fluidRow(
shiny::column(6,shiny::checkboxGroupInput(inputId = "BoolExp",
label = "Detect expirations phases",
choiceNames = c("TRUE"), choiceValues = c(TRUE))),
shiny::column(6,shiny::numericInput(inputId = "mzBreathTracer",label = "mzBreathTracer",value = 59.049))
),
#saveDir
shiny::fluidRow(
shiny::p(class = 'text-center',
shiny::actionButton(inputId = "createPtrSet",label = "create a PtrSet")
))
)
} else {
shiny::fluidRow(
shiny::p(class = 'text-center',
shiny::actionButton("selectFile","Choose a .Rdata ptrSet object"))
)
}
})
### Choose a directory ----
shiny::observeEvent(input$selectDir, {
pth <- utils::choose.dir() #tk_choose.dir
paramRv$path<-pth
})
### Display the choosen directory ----
output$showDirectorySelect<-shiny::renderPrint({
if(!is.null(paramRv$path)) print(paramRv$path)
})
### Création d'un directory si selection de createPtrSet ----
shiny::observeEvent(input$createPtrSet, {
if(!is.null(input$BoolExp)) fracMaxTIC<-0.7 else fracMaxTIC <- 0
ptrSet<-createPtrSet(dir = paramRv$path , setName = input$ptrName,
mzCalibRef = c(input$mz1,input$mz2,input$mz3,input$mz4,input$mz5),
fracMaxTIC = fracMaxTIC,
mzBreathTracer = input$mzBreathTracer, saveDir = paramRv$path)
rv$ptrset<-ptrSet
rv$new <-TRUE
})
shiny::observeEvent(input$selectFile, {
pth <- file.choose()
load_obj <- function(f){
env <- new.env()
nm <- load(f, env)[1]
env[[nm]]
}
rv$ptrset<-load_obj(pth)
rv$new <- TRUE
})
## Serveur Affichage du Ptrset ----
output$showPtrSet<-shiny::renderPrint(
if(!is.null(rv$ptrset)) print(rv$ptrset)
)
## Serveur Tracé du Ptrset ----
output$plotPtrSet <- shiny::renderPlot({
if(!is.null(rv$ptrset)) plot(rv$ptrset)
})
## Fonction serveur bouton Update Ptrset
output$update<- shiny::renderUI({
if(!is.null(rv$ptrset)) shiny::actionButton(inputId = "updatePtrSet",label = "Update ptrSet")
})
shiny::observeEvent(input$updatePtrSet,{
if(!is.null(rv$ptrset)){
rv$ptrset<-updatePtrSet(rv$ptrset)
rv$new <-TRUE
}
})
##UI output "paramTimeLimit" lorsque on a un ptrset ----
output$paramTimeLimit<-shiny::renderUI({
if(!is.null(rv$ptrset)){
shiny::fluidPage(
#choose file in the ptrSet
shiny::fluidRow(
if (rv$new){
shiny::selectInput("fileName","File name:",as.list(names(getTimeInfo(rv$ptrset)$TIC)),selected = FALSE,selectize=FALSE)
}
else {
shiny::selectInput("fileName","File name:",as.list(names(getTimeInfo(rv$ptrset)$TIC)),selected = input$fileName ,selectize=FALSE)
}
),
#UI rentrer les valeurs des paramètres
shiny::fluidRow(shiny::h5(shiny::strong("Parameters :"))),
# if (rv$newFile) {
# shiny::fluidRow(
#
# shiny::column(width = 6,shiny::numericInput("fracMaxTIC", "FracMaxTIC", 0.8 ,0, 1, 0.05)),
# shiny::column(width = 6,shiny::numericInput("fracMaxTICBg", "FracMaxTICBg",0.2,0, 1, 0.05)),
# shiny::column(width = 6,shiny::numericInput("derivThresholdExp", "DerivThresholdExp", 1, 0, 5, 0.05)),
# shiny::column(width = 6,shiny::numericInput("derivThresholdBg", "DerivThresholdBg",0.05,0, 2, 0.05)),
# shiny::column(width = 6,shiny::numericInput("minPoints", "MinPoints", 1, 1, 10, 1)),
# shiny::column(width = 6,shiny::numericInput("degreeBaseline", "DegreeBaseline", 1, 1, 30, 1)),
# shiny::column(width = 6,shiny::numericInput("knotsPeriod", "KnotsPeriod",
# 3, 1, 10, 1)),
# shiny::column(width = 10,shiny::selectInput(inputId = "methodKnot",
# label = "Method for knot location ",
# choices = c("Around expiration",
# "Uniform"),
# multiple = FALSE))
# )
# }
shiny::fluidRow(
shiny::column(width = 6,shiny::numericInput("fracMaxTIC", "FracMaxTIC", rv$ptrset@parameter$timeLimit$fracMaxTIC,0, 1, 0.05)),
shiny::column(width = 6,shiny::numericInput("fracMaxTICBg", "FracMaxTICBg",rv$ptrset@parameter$timeLimit$fracMaxTICBg,0, 1, 0.05)),
shiny::column(width = 6,shiny::numericInput("derivThresholdExp", "DerivThresholdExp", rv$ptrset@parameter$timeLimit$derivThresholdExp, 0, 5, 0.05)),
shiny::column(width = 6,shiny::numericInput("derivThresholdBg", "DerivThresholdBg",rv$ptrset@parameter$timeLimit$derivThresholdBg,0, 2, 0.05)),
shiny::column(width = 6,shiny::numericInput("minPoints", "MinPoints", rv$ptrset@parameter$timeLimit$minPoints, 1, 10, 1)),
shiny::column(width = 6,shiny::numericInput("degreeBaseline", "DegreeBaseline", rv$ptrset@parameter$timeLimit$degreeBaseline, 1, 30, 1)),
shiny::column(width = 6,shiny::numericInput("knotsPeriod", "KnotsPeriod",
rv$ptrset@parameter$knotsPeriod, 1, 10, 1)),
shiny::column(width = 10,shiny::selectInput(inputId = "methodKnot",
label = "Method for knot location ",
choices = c("Around expiration",
"Uniform"),
multiple = FALSE))
)
,
# delete des expirations et d'appliquer les changements de paramètres sur les expirations
shiny::fluidRow(
shiny::actionButton('reset', 'Apply for this file'),
shiny::actionButton('resetAll', 'Apply for all')),
shiny::p(class='text-center', shiny::actionButton('delete',
'Delete selected rows')
)
)
}
},quoted=FALSE)
# output$nomFile<-shiny::renderUI({
# if(!is.null(rv$ptrset && rv$new) ){
# shiny::fluidPage(
#
# #choose file in the ptrSet
# shiny::fluidRow(
# shiny::selectInput("fileName","File name:",as.list(names(rv$ptrset@TIC)),selectize=FALSE)
# ))
# }
# }
# )
#rv <- shiny::reactiveValues( data = NULL , bgPoints=NULL, ptrset= ptrSet )
# get the time limit of the selected file
#rv<-list()
shiny::observeEvent(input$fileName, {
if(!is.null(rv$ptrset)){
rv$data <- t(getTimeInfo(rv$ptrset)$timeLimit[[input$fileName]]$exp)
rv$bgPoints <- getTimeInfo(rv$ptrset)$timeLimit[[input$fileName]]$backGround
rv$knots<- getPeaksInfo(rv$ptrset)$knots[[input$fileName]]
rv$new <-FALSE
rv$newFile <-TRUE
}
})
#display time limit table
output$tableTimeLimit <- DT::renderDataTable( {
if(!is.null(rv$ptrset) & !is.null(input$fileName)){
#fileName<-input$fileNameTimeLimit
#indexTimeLimit <- rv$ptrset@timeLimit[[fileName]]$exp
DT::datatable(rv$data, editable = TRUE,
selection=list(target="row"),
rownames=as.character(seq(1,nrow(rv$data)))
)
}
})
### delete the selected expirations ----
shiny::observeEvent(input$delete, {
rowNum <- input$tableTimeLimit_rows_selected
if(length(rowNum) == nrow(rv$data)){
shiny::showNotification("At least one period must be selected",
duration = NULL, id="warnings" )
}else {
#shiny::removeNotification("warnings")
expirationTodelete<-rv$data[rowNum,,drop=FALSE]
knots<-rv$knots
knotTodelete<-Reduce(c,apply(expirationTodelete,1,
function(x) which(x[1] <= knots &
knots <= x[2])))
rv$data <- rv$data[-rowNum,,drop=FALSE]
rv$knots<-knots[-knotTodelete]
ptrSetTemp<-rv$ptrset
timeLimitInput<-getTimeInfo(ptrSetTemp)$timeLimit[[input$fileName]]
timeLimitInput$exp <- t(rv$data)
ptrSetTemp<-setTimeLimits(ptrSetTemp,newTimeLimites =timeLimitInput,index = input$fileName )
#ptrSetTemp<-setKnots(ptrSetTemp,rv$knots,input$fileName)
rv$ptrset<-ptrSetTemp
#ptrSetNew(ptrSet)
}
})
### reset the expirations with timeLimit function for the current file ----
shiny::observeEvent(input$reset, {
shiny::removeNotification("warnings")
fracMaxTICNew <- input$fracMaxTIC
##default value
fracMaxTICBgNew <- input$fracMaxTICBg
derivThresholdExpNew <- input$derivThresholdExp
derivThresholdBgNew <-input$derivThresholdBg
minPointsNew <-input$minPoints
degreeBaselineNew <- input$degreeBaseline
timeLimit<-timeLimitFun(TIC = getTimeInfo(rv$ptrset)$breathTracer[[input$fileName]],
fracMaxTIC =fracMaxTICNew ,
fracMaxTICBg = fracMaxTICBgNew,
derivThresholdExp = derivThresholdExpNew,
derivThresholdBg = derivThresholdBgNew,
minPoints =minPointsNew ,
degreeBaseline = degreeBaselineNew)
t<-as.numeric(names( getTimeInfo(rv$ptrset)$TIC[[input$fileName]]))
background<-timeLimit$backGround
if(input$methodKnot == "Around expiration")
method<-"expiration" else method<- "uniform"
knots<-try(defineKnotsFunc(t,background,input$knotsPeriod,method))
rv$data <- t(timeLimit$exp)
rv$bgPoints<- timeLimit$backGround
rv$knots<-knots
timeLimitInput<-getTimeInfo(rv$ptrset)$timeLimit[[input$fileName]]
timeLimitInput$exp <- t(rv$data)
timeLimitInput$backGround <- rv$bgPoints
rv$ptrset<-setTimeLimits(rv$ptrset,newTimeLimites =timeLimitInput,index = input$fileName )
rv$ptrset<-setKnots(rv$ptrset,rv$knots,input$fileName)
paramterTimeLimit<-list(fracMaxTIC=fracMaxTICNew,
fracMaxTICBg=fracMaxTICBgNew,
derivThresholdExp=derivThresholdExpNew,
derivThresholdBg=derivThresholdBgNew,
minPoints = minPointsNew,
degreeBaseline=degreeBaselineNew)
parameter<-getParameters(rv$ptrset)
parameter$knotsPeriod<-input$knotsPeriod
parameter$timeLimit<-paramterTimeLimit
rv$ptrset<- setParameters(rv$ptrset,parameter)
rv$new <-FALSE
rv$newFile <-FALSE
})
### reset the expirations with timeLimit function for all file ----
shiny::observeEvent(input$resetAll, {
#shiny::removeNotification("warnings")
fracMaxTICNew <- input$fracMaxTIC
##default value
fracMaxTICBgNew <- input$fracMaxTICBg
derivThresholdExpNew <- input$derivThresholdExp
derivThresholdBgNew <-input$derivThresholdBg
minPointsNew <-input$minPoints
degreeBaselineNew <- input$degreeBaseline
timeLimit<-lapply(names(getTimeInfo(rv$ptrset)$TIC),function(fileName) {
timeLimitFun(TIC = getTimeInfo(rv$ptrset)$breathTracer[[fileName]],
fracMaxTIC =fracMaxTICNew ,
fracMaxTICBg = fracMaxTICBgNew,
derivThresholdExp = derivThresholdExpNew,
derivThresholdBg = derivThresholdBgNew,
minPoints =minPointsNew ,degreeBaseline = degreeBaselineNew)
})
names(timeLimit) <- names(getTimeInfo(rv$ptrset)$TIC)
knots<-lapply(names(getTimeInfo(rv$ptrset)$timeLimit),function(fileName) {
background<-timeLimit[[fileName]]$backGround
t<-as.numeric(names( getTimeInfo(rv$ptrset)$TIC[[fileName]]))
if(input$methodKnot == "Around expiration") {
defineKnotsExpiration(t,background,input$knotsPeriod)
} else {
unique(c(t[1],
seq(t[1],utils::tail(t,1),by=input$knotsPeriod),
utils::tail(t,1)))
}
})
names(knots)<-names(timeLimit)
rv$data <- t(timeLimit[[input$fileName]]$exp)
rv$bgPoints<- timeLimit[[input$fileName]]$backGround
rv$knots<-knots[[input$fileName]]
rv$ptrset<-setTimeLimits(rv$ptrset,timeLimit)
rv$ptrset<-setKnots(rv$ptrset,knots)
paramterTimeLimit<-list(fracMaxTIC=fracMaxTICNew,
fracMaxTICBg=fracMaxTICBgNew,
derivThresholdExp=derivThresholdExpNew,
derivThresholdBg=derivThresholdBgNew,
minPoints = minPointsNew,
degreeBaseline=degreeBaselineNew)
parameter<-getParameters(rv$ptrset)
parameter$knotsPeriod<-input$knotsPeriod
parameter$timeLimit<-paramterTimeLimit
rv$ptrset<- setParameters(rv$ptrset,parameter)
})
# display the expirations in data table ----
output$table <- DT::renderDataTable( {
if(!is.null(rv$data))
#shiny::removeNotification("warnings")
DT::datatable(rv$data, editable = TRUE,
selection=list(target="row"),
rownames=as.character(seq(1,nrow(rv$data)))
)
})
shiny::observeEvent(input$tableTimeLimit_cell_edit,
{
rv$data[ input$tableTimeLimit_cell_edit$row ,
input$tableTimeLimit_cell_edit$col] <- as.numeric(input$tableTimeLimit_cell_edit$value)
timeLimitInput<-getTimeInfo(rv$ptrset)$timeLimit[[input$fileName]]
timeLimitInput$exp <- t(rv$data)
rv$ptrset<-setTimeLimits(rv$ptrset,newTimeLimites =timeLimitInput,index = input$fileName )
}
)
# PlotTimeLimit ----
output$plotTimeLimit <- plotly::renderPlotly({
if(!is.null(rv$ptrset) & !is.null(input$fileName) & !is.null(rv$data)){
s <- input$tableTimeLimit_rows_selected
fileName <- input$fileName
TIC <- getTimeInfo(rv$ptrset)$breathTracer[[fileName]]
time <- as.numeric(names(TIC))
indexTimeLimit <- t(rv$data)
#indexTimeLimit <- rv$ptrset@timeLimit[[fileName]]$exp
expPoint<-Reduce(c,apply(indexTimeLimit,2,function(x) seq(x[1],x[2])))
bgPoint<-rv$bgPoints
#bgPoint<-rv$ptrset@timeLimit[[fileName]]$backGround
knots<-rv$knots
p <- ggplot2::qplot(x=time,y=TIC,
xlab="time",ylab="intensity",
main=paste("Trace of",input$fileName))
if(!is.null(expPoint))
p<-p+ggplot2::geom_point(mapping=ggplot2::aes(time ,y,colour=point),
data=data.frame(time= time[expPoint],y=TIC[expPoint],point="exp"))
if(!is.null(bgPoint))
p<-p + ggplot2::geom_point(mapping=ggplot2::aes(time ,y,colour=point),
data=data.frame(time= time[bgPoint],y=TIC[bgPoint],point="Background"))
p <- p + ggplot2::theme_classic()
if(!is.null(knots)){
p<- p + ggplot2::geom_point(mapping=ggplot2::aes(time ,y,colour=point),
data=data.frame(time= knots,
y=rep(0,length(knots)),
point="knots"),shape=4) +
ggplot2::ggtitle(paste("Trace of",input$fileName,length(knots)))
}
if( length(s) ){
s <- s[s<=ncol(indexTimeLimit)] #to avoid warnings
expirationSelect<-Reduce(c,apply(indexTimeLimit[,s,drop=FALSE],2,function(x) seq(x[1],x[2])))
if(length(s)) p <- p +
ggplot2::geom_point(mapping=ggplot2::aes(time ,y,colour=point),
data=data.frame(time= time[expirationSelect],
y=TIC[expirationSelect],
point="Expiration selected"))
p<- p + ggplot2::scale_colour_manual(values = c("#F8766D","#7CAE00",
"#C77CFF","#00BFC4"))
}
plotly::ggplotly(p)
}
})
# Calibration ----
output$paramCalib<- shiny::renderUI({
if(!is.null(rv$ptrset)){
shiny::fluidPage(
shiny::fluidRow(
shiny::selectInput("fileNameCalib","File name:",as.list(names(rv$ptrset@TIC)),selectize=FALSE),
shiny::fluidRow(shiny::h4("Calibration masses"),
shiny::h6("To remove a mass, put its value to 0. At least two masses are required") ),
),
# shiny::fluidRow(shiny::h5(strong(length(rv$ptrset@parameter$mzCalibRef)))),
# shiny::fluidRow(shiny::h4("Calibration masses"),
#
# shiny::column(4,shiny::numericInput(inputId = "mz1New",label = "mz1",value = rv$ptrset@parameter$mzCalibRef[1])),
# shiny::column(4,shiny::numericInput(inputId = "mz2New",label = "mz2",value =rv$ptrset@parameter$mzCalibRef[2])),
# shiny::column(4,shiny::numericInput(inputId = "mz3New",label = "mz3",value = rv$ptrset@parameter$mzCalibRef[3])),
# shiny::column(4,shiny::numericInput(inputId = "mz4New",label = "mz4",value = rv$ptrset@parameter$mzCalibRef[4]))
# ),
)
}
})
output$paramCalib2<- shiny::renderUI({
if(!is.null(rv$ptrset)){
lapply(1:length(rv$ptrset@parameter$mzCalibRef), function(i) {
output[[paste0('b', i)]] <- shiny::renderUI({
shiny::fluidRow(
#Affichage des nouvelles masses
shiny::numericInput(inputId = paste0("mz", i,"New"), label = paste("mz", i), value = rv$ptrset@parameter$mzCalibRef[i]),
# #Boutons pour effacer les masses
# shiny::actionButton(inputId = paste0("close", i),label="X")
)
})
})
}
})
output$paramCalib3<- shiny::renderUI({
if(!is.null(rv$ptrset)){
shiny::fluidPage(
shiny::fluidRow(
shiny::p(class='text-center',
shiny::actionButton("resetCalib",label = "Reset calibration"))
)
# shiny::fluidRow(
# shiny::p(class='text-center',
# shiny::actionButton("addCalib",label = "Add calibration"))
# )
)
}
})
output$paramCalib4 <- shiny::renderUI({
if(!is.null(rv$ptrset)){
shiny::fluidPage(
shiny::fluidRow(
shiny::p(class='text-center',
shiny::actionButton("addMassButton","Add mass"))
)
)
}
})
# masse <- eventReactive(input$addMassButton,{
# if(!is.null(rv$ptrset)){
# #shiny::numericInput(inputId = "IdAddedMass", label = paste("mz", length(rv$ptrset@parameter$mzCalibRef)+1), value = 60)
# #print(input$IdAddedMass)
# #rv$ptrset@parameter$mzCalibRef[[length(rv$ptrset@parameter$mzCalibRef)+1]] <- input$IdAddedMass
# rv$ptrset@parameter$mzCalibRef[[length(rv$ptrset@parameter$mzCalibRef)+1]] <- 0
#
# }
# })
#
# output$addMass_UI <- renderUI({
# masse()
# })
# Reset Calib
shiny::observeEvent(input$resetCalib,{
mzCalibRef = c()
for (i in 1:length(rv$ptrset@parameter$mzCalibRef)){
if (eval(parse(text=paste0("input$mz",i,"New!=0")))){
mzCalibRef <-c(mzCalibRef,eval(parse(text=paste0("input$mz",i,"New"))))
}
}
rv$ptrset<-calibration(rv$ptrset,mzCalibRef)
})
# Add Mass initialisée à 0
shiny::observeEvent(input$addMassButton,{
rv$ptrset@parameter$mzCalibRef[length(rv$ptrset@parameter$mzCalibRef)+1] <- 0
})
# shiny::observeEvent( function(i){
#
#
# input$closei
# {
# rv$ptrset@parameter$mzCalibRef <- rv$ptrset@parameter$mzCalibRef[-length(rv$ptrset@parameter$mzCalibRef)]
# }
# }
# )
# # Close mass
# shiny::observeEvent( input$close3, {
# print(length(rv$ptrset@parameter$mzCalibRef))
# rv$ptrset@parameter$mzCalibRef <- rv$ptrset@parameter$mzCalibRef[-3]
#
# }
#
# )
output$plotCalib<- shiny::renderPlot({
if(!is.null(rv$ptrset)) plotCalib(rv$ptrset,file=input$fileNameCalib)
})
# shiny::observeEvent(input$close, {
# shiny::stopApp(ptrSet)
# })
#
# Détection des pics ----
shiny::observeEvent(input$detectPeak, {
ptrSet<-rv$ptrset
resolution<-c(as.numeric(input$resMin),
as.numeric(input$resMean),
as.numeric(input$resMax))
rv$ptrset<-detectPeak(rv$ptrset,ppm = as.numeric(input$PPM),
minIntensity =as.numeric(input$minIntensity) ,
resolutionRange =NULL )
rv$ptrset<-rv$ptrset
})
## Choix du fichier ----
output$secondSelectionFileRawData<-shiny::renderUI({
if(!is.null(rv$ptrset)){
shiny::fluidPage( shiny::selectInput(inputId = "plotRaw",label = "File to plot",
choices= c(names(rv$ptrset@peakList)),
selectize=FALSE)
)
}
})
# Choix du feature ----
output$secondSelectionMzRawData<-shiny::renderUI({
if(!is.null(rv$ptrset) & !is.null(input$plotRaw)){
shiny::fluidPage( shiny::selectInput(inputId = "plotRawmz",label = "features",
choices= c(rownames(Biobase::exprs(rv$ptrset@peakList[[input$plotRaw]]))),
selectize=FALSE)
)
}
})
# Plot de détection de peaks ----
output$RawData<-shiny::renderPlot({
if(!is.null(rv$ptrset)){
if(!is.null(input$plotRawmz)){
peakList<-Biobase::fData(getPeakList(rv$ptrset)[[input$plotRaw]])
peaksParam <- peakList[as.character(input$plotRawmz),
c("Mz","parameterPeak.delta1",
"parameterPeak.delta2",
"parameterPeak.height")]
fctFit <- rv$ptrset@fctFit[[input$plotRaw]]
peakShape<-rv$ptrset@peakShape[[input$plotRaw]]
peaks <- function(mz) eval(parse(text = paste0("ptairMS:::",fctFit)))(peaksParam[1,"Mz"],
peaksParam[1,"parameterPeak.delta1"],
peaksParam[1,"parameterPeak.delta2" ],
peaksParam[1,"parameterPeak.height"],
mz,
peakShape)
temporalEstim<- Biobase::exprs(getPeakList(rv$ptrset)[[input$plotRaw]])[as.character(input$plotRawmz),]
fileFullName<- getFileNames(rv$ptrset,fullNames =TRUE )[ getFileNames(rv$ptrset)==input$plotRaw]
g<-plotPeakRaw(set = rv$ptrset,mzRange = as.numeric(input$plotRawmz),
file=fileFullName,peaks = peaks,fctFit=fctFit,temporalEstim = temporalEstim,
ppm = 700)
print(g)
}
}
})
output$group <-shiny::renderUI({
if(!is.null(rv$ptrset)){
shiny::fluidPage(shiny::selectInput(inputId = "group",label = "Select group",
choices= c("NULL",colnames(rv$ptrset@sampleMetadata)),
selectize=FALSE))
}
})
#
shiny::observeEvent(input$align, {
ptrSet<-rv$ptrset
pValThres<-input$pValThres
group<-NULL
if(input$group!="NULL") group<-input$group
eSet<- ptairMS::alignSamples(ptrSet,ppmGroup = 90,fracGroup = 1- input$fracGroup ,group = group,
pValGreaterThres = pValThres,pValLessThres = pValThres,
fracExp = input$fracExp,quantiUnit=input$quantiUnit)
rv$eset<-eSet
})
output$nbPeak <- shiny::renderText({
if(!is.null( rv$eset)){
X<-Biobase::exprs(rv$eset)
paste(nrow(X),"peaks aligned")
}
})
output$tableAlign<- plotly::renderPlotly({
if(!is.null( rv$eset)){
X<-Biobase::exprs(rv$eset)
if(input$Transformation == "log2"){
X<-log2(X)
} else if (input$Transformation == "Centred reduced"){
X<-t(apply(X,1,function(x) (x-mean(x,na.rm=TRUE))/sd(x,na.rm=TRUE)))
}
Y<-Biobase::pData(rv$eset)
#ropls::imageF(log2(Biobase::exprs(rv$eset)))
plotly::plot_ly(z = X,
x = substr(colnames(Biobase::exprs(rv$eset)),1,7),
y = paste0("mz-",as.character(rownames(Biobase::exprs(rv$eset)))),
type = "heatmap", colorscale='Jet')
}
})
shiny::observeEvent(input$impute,{
if(!is.null(rv$eset) & !is.null(rv$ptrset)){
rv$eset <- impute(eSet = rv$eset,ptrSet = rv$ptrset,parallelize = FALSE)
}
})
output$secondSelectionLongitudinal<-shiny::renderUI({
if(!is.null(rv$ptrset) & !is.null(rv$eset)){
shiny::fluidPage(
shiny::selectInput("mzLongotudinal","Feature",
rownames(Biobase::exprs(rv$eset)),
selectize=FALSE),
shiny::selectInput("idPatient","idPatient",
c("None",colnames(rv$ptrset@sampleMetadata)),
selectize=FALSE),
shiny::selectInput("timeColumn","x-axis",
c("None",colnames(rv$ptrset@sampleMetadata)),
selectize=FALSE),
shiny::selectInput("columnLongitudinal","Colored by:",
c("None",colnames(rv$ptrset@sampleMetadata)),
selectize=FALSE) )
}
})
output$dataLongitudinal<-plotly::renderPlotly({
if(!is.null(rv$eset) ){
if(!is.null(input$timeColumn) & !is.null(input$columnLongitudinal)){
if(input$timeColumn != "None" & input$columnLongitudinal != "None"){
X<-Biobase::exprs(rv$eset)
Y<-Biobase::pData(rv$eset)
mz<-input$mzLongotudinal
colTime<-input$timeColumn
colorby<-input$columnLongitudinal
name<-input$idPatient
Y$file<-rownames(Y)
quanti<-Biobase::annotation(rv$eset)
g <- ggplot2::ggplot()
for(j in unique(Y[,name])){
if(all(!is.na(Y[Y[,name] == j,colTime]))){
g <- g+ suppressWarnings(ggplot2::geom_line(ggplot2::aes(x=timeC,y=cps,color=filter,label=files,group=name),
data=data.frame(timeC =Y[Y[,name] == j,colTime],
cps=X[as.character(mz),Y[,name]==j],
filter=Y[Y[,name] == j,colorby],
files=rownames(Y)[Y[,name] == j],
name=j))) +
suppressWarnings(ggplot2::geom_point(ggplot2::aes(x=timeC,y=cps,color=filter,label=files),
data=data.frame(timeC=Y[Y[,name] == j,colTime],
cps=X[as.character(mz),Y[,name]==j],
filter=Y[Y[,name] == j,colorby],
files=rownames(Y)[Y[,name] == j],
name=j)))
}
}
g<-g + ggplot2::ggtitle(mz,annotateVOC(as.numeric(mz),ppm=100)[3]) +
ggplot2::labs(y= quanti, x = colTime )
`%>%` <- plotly::`%>%`
plotly::ggplotly(g) %>%
plotly::layout(title = list(text = paste0(mz,
'<br>',
'<sup>',
annotateVOC(as.numeric(mz),ppm=100)[3],
'</sup>')))
}
}
}
})
output$pca<-shiny::renderUI({
if(!is.null(rv$ptrset)){
shiny::fluidPage(
shiny::selectInput("colorPca","Colored by:",
colnames(rv$ptrset@sampleMetadata),
selectize=FALSE)
)
}
})
output$pcaMarker<-shiny::renderUI({
if(!is.null(rv$ptrset)){
shiny::fluidPage(
shiny::selectInput("markerPca","Marker:",
c("sampleNames",colnames(rv$ptrset@sampleMetadata)),
selectize=FALSE)
)
}
})
#plot acps
output$acp <- plotly::renderPlotly({
if(!is.null(rv$eset) & !is.null(input$markerPca) ){
# getting Shiny parameters
eset <- rv$eset
# log2 transformation
X<-Biobase::exprs(eset)
X[X<0]<-min(X[X>0],na.rm=FALSE)
Biobase::exprs(eset) <- log2(X)
set.pca <- ropls::opls(eset, predI = 2, info.txtC = "none", fig.pdfC = "none",
crossvalI =4)
rv$pca<-set.pca
if( !is.na(input$x) & !is.na(input$y)){
if(input$x !=input$y){
score_plotly(set.pca,
components.vi = c(input$x, input$y),
label.c = input$markerPca,
color.c = input$colorPca,
ellipse.l = FALSE,
palette.c = "",
#info.vc = c("sampleNames",color),
size.ls = list(legend_title.i = 8,
legend_text.i = 8))
}
}
}
})
output$getLoading<-shiny::renderTable({
if(!is.null(rv$pca)){
X<-Biobase::exprs(rv$eset)
importance<-ropls::getLoadingMN(rv$pca)
tx<-rownames(X)[order(importance[,input$x]^2,decreasing = TRUE)[seq_len(input$maxRow)]]
ty<-rownames(X)[order(importance[,input$y]^2,decreasing = TRUE)[seq_len(input$maxRow)]]
data<-cbind(mz.tx=tx,annotation.tx=ptairMS::annotateVOC(as.numeric(tx))[,3],
mz.ty=ty,annotation.ty=ptairMS::annotateVOC(as.numeric(ty))[,3])
colnames(data)<-gsub(pattern = "x",replacement = input$x,x = colnames(data) )
colnames(data)<-gsub(pattern = "y",replacement = input$y,x = colnames(data) )
data
}
})
}
shiny::shinyApp(ui = ui, server = server)
}
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.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.