R/shinyApp.R
In PlantDefenseMetabolism/MetCirc: Navigating mass spectral similarity in high-resolution MS/MS metabolomics data
#' @import grDevices
#' @import graphics
#' @name shinyCircos
#' @title Interactive visualisation of similarity and navigation of MS/MS features
#' @description Visualise the similarity of MS/MS features in a reactive
#' context. See \code{Details} the vignette for further descriptions on how to use
#' \code{shinyCircos}.
#' @usage shinyCircos(similarityMatrix, msp = NULL, ...)
#' @param similarityMatrix \code{matrix}, \code{similarityMatrix} contains
#' pair-wise similarity coefficients which give information about the similarity
#' between MS/MS features
#' @param msp \code{MSP}, an S4 object of class \code{MSP}, the
#' \code{MSP}-object will be used to display information about the selected
#' feature
#' @param ... further arguments passed to \code{shinyCircos}, e.g.
#' \code{cexFeatureNames} to pass to \code{plotCircos} to set font size in
#' \code{plotCircos} of feature names
#' @details The function is based on the \code{shiny} and \code{circlize} package.
#' The user can choose interactively thresholds, type of links (between or
#' within groups), display information about MS/MS features, permanently select
#' MS/MS features and export selected precursors. When running
#' \code{shinyCircos} with the object of class \code{MSP}, annotation data of
#' selected MS/MS features will be displayed.
#' @return \code{shinyCircos} returns a \code{character} vector with the
#' (permanently) selected precursors or an object with the entries \code{msp}
#' and \code{selectedFeatures} if a \code{MSP}-object was passed to
#' \code{shinyCircos}
#' @author Thomas Naake, \email{thomasnaake@@googlemail.com}
#' @examples
#' data("idMSMStoMSP", package = "MetCirc")
#' ## truncate files
#' finalMSP <- finalMSP[c(1:20, 29:48, 113:132, 240:259)]
#' data("binnedMSP", package = "MetCirc")
#' binnedMSP <- binnedMSP[c(1:20, 29:48, 113:132, 240:259),]
#' similarityMat <- createSimilarityMatrix(binnedMSP)
#' \dontrun{shinyCircos(similarityMatrix = similarityMat, msp = finalMSP)}
#' @export
shinyCircos <- function(similarityMatrix, msp = NULL, ...) {
if (!is.null(msp)) if (class(msp) != "MSP") stop("msp is not of class MSP")
## circlize parameters
circos.par(gap.degree = 0, cell.padding = c(0, 0, 0, 0),
track.margin = c(0.0, 0))
groupname <- rownames(similarityMatrix)
## create plots and assign to objects by recordPlot
## rt
simMatRT <- createOrderedSimMat(similarityMatrix, order = "retentionTime")
link0MatRT <- createLink0Matrix(simMatRT)
groupnameRT <- rownames(simMatRT)
plotCircos(groupnameRT, NULL, initialize=TRUE, featureNames = TRUE,
groupSector = TRUE, groupName = FALSE, links = FALSE,
highlight = FALSE, ...)
PlotFilledRT <- recordPlot()
## get group and name from groupnameRT argument
## groupnameRT is a vector containing information about group and name,
## where group is the first element and name the last element separated by _
groupRT <- lapply(strsplit(groupnameRT, split = "_"), "[", 1)
groupRT <- unlist(groupRT)
nameRT <- lapply(strsplit(groupnameRT, split = "_"), function (x) x[length(x)])
nameRT <- unlist(nameRT)
## get degree of features
degreeFeaturesRT <- lapply(groupnameRT,
function(x) mean(circlize:::get.sector.data(x)[c("start.degree", "end.degree")]))
plot.new()
plotCircos(groupnameRT, NULL, initialize=TRUE, featureNames = TRUE,
groupSector = TRUE, groupName = FALSE, links = FALSE,
highlight = TRUE, ...)
PlotHighlightRT <- recordPlot()
plot.new()
## mz
simMatMZ <- createOrderedSimMat(similarityMatrix, order = "mz")
link0MatMZ <- createLink0Matrix(simMatMZ)
groupnameMZ <- rownames(simMatMZ)
plotCircos(groupnameMZ, NULL, initialize=TRUE, featureNames = TRUE,
groupSector = TRUE, groupName = FALSE, links = FALSE,
highlight = FALSE, ...)
PlotFilledMZ <- recordPlot()
## get group and name from groupnameMZ argument
## groupnameMZ is a vector containing information about group and name,
## where group is the first element and name the last element separated by _
groupMZ <- lapply(strsplit(groupnameMZ, split = "_"), "[", 1)
groupMZ <- unlist(groupMZ)
nameMZ <- lapply(strsplit(groupnameMZ, split = "_"), function (x) x[length(x)])
nameMZ <- unlist(nameMZ)
## get degree of features
degreeFeaturesMZ <- lapply(groupnameMZ,
function(x) mean(circlize:::get.sector.data(x)[c("start.degree", "end.degree")]))
plot.new()
plotCircos(groupnameMZ, NULL, initialize=TRUE, featureNames = TRUE,
groupSector = TRUE, groupName = FALSE, links = FALSE,
highlight = TRUE, ...)
PlotHighlightMZ <- recordPlot()
plot.new()
## clustering
simMatClustering <- createOrderedSimMat(similarityMatrix,
order = "clustering")
link0MatClustering <- createLink0Matrix(simMatClustering)
groupnameClustering <- rownames(simMatClustering)
plotCircos(groupnameClustering, NULL, initialize=TRUE,
featureNames = TRUE, groupSector = TRUE, groupName = FALSE,
links = FALSE, highlight = FALSE, ...)
PlotFilledCluster <- recordPlot()
## get group and name from groupnameMZ argument
## groupnameMZ is a vector containing information about group and name,
## where group is the first element and name the last element separated by _
groupClustering <- lapply(strsplit(groupnameClustering, split = "_"), "[", 1)
groupClustering <- unlist(groupClustering)
nameClustering <- lapply(strsplit(groupnameClustering, split = "_"),
function (x) x[length(x)])
nameClustering <- unlist(nameClustering)
## get degree of features
degreeFeaturesClust <- lapply(groupnameClustering,
function(x) mean(circlize:::get.sector.data(x)[c("start.degree", "end.degree")]))
plot.new()
plotCircos(groupnameClustering, NULL, initialize=TRUE, featureNames = TRUE,
groupSector = TRUE, groupName = FALSE, links = FALSE,
highlight = TRUE, ...)
PlotHighlightCluster <- recordPlot()
plot.new()
ui <- fluidPage(
tags$head(tags$script('
$(document).on("shiny:connected", function(e) {
Shiny.onInputChange("innerWidth", window.innerWidth);
});
$(window).resize(function(e) {
Shiny.onInputChange("innerWidth", window.innerWidth);
});
'
)),
column(4,
fluidRow(
tabsetPanel(id = "tabs",
tabPanel("Main", wellPanel(
radioButtons("choiceLinks", "choose type of links",
choices = c("all" = "all", "inter-class links" = "inter",
"intra-class links" = "intra"),
selected = "all"),
sliderInput("threshold",
"Threshold for similarity to display",
min = 0, max = 1, value = c(0.8, 1)),
radioButtons("order", "order within groups",
choices = c("clustering" = "clustering",
"m/z" = "mz", "retention time" = "retentionTime"),
selected = "mz"),
uiOutput("annotationName"),
uiOutput("annotationClass"),
uiOutput("annotationInformation"),
uiOutput("annotationAdduct"),
uiOutput("annotationButton"),
actionButton("resetClickIndices", "Reset features"),
actionButton("stop", "Stop and export \n selected features")
)),
tabPanel("Appearance", wellPanel(
sliderInput("plotSize", "plot size",
min = 0.5, max = 1.5, value = 1),
sliderInput("precision", "precision of numbers", value = 2, min = 0, max = 5, step = 1),
checkboxInput("legend", "legend", value = FALSE)
))
)
),
plotOutput("circosLegend", height = "300")
),
column(8,
fluidRow(uiOutput("sized_plot")),
fluidRow(
verbatimTextOutput("dimension_display"),
htmlOutput("clickConnectedFeature"),
verbatimTextOutput("dblClickFeature")
)
)
)
server <- function(input, output, session) {
## annotation
if(!is.null(msp)) {mspannotation <- reactiveValues(
names = msp@names, information = msp@information,
classes = msp@classes, adduct = msp@adduct)}
output$annotationName <- renderUI({
if (!is.null(msp)) {
if (length(indClick$ind) > 0 && onCircle$is) {
textInput("names", label = "name",
value = isolate(names(MSP())[indMSP()]))
} else NULL
}
})
output$annotationClass <- renderUI({
if (!is.null(msp)) {
if (length(indClick$ind) > 0 && onCircle$is) {
textInput("classes", label = "class",
value = isolate(classes(MSP())[indMSP()]))
} else NULL
}
})
output$annotationInformation <- renderUI({
if (!is.null(msp)) {
if (length(indClick$ind) > 0 && onCircle$is) {
#if (onCircle$is) {
textInput("information", label = "information",
value = isolate(information(MSP())[indMSP()]))
} else NULL
}
})
output$annotationAdduct <- renderUI({
if (!is.null(msp)) {
if (length(indClick$ind) > 0 && onCircle$is) {
textInput("adduct", label = "adduct",
value = isolate(adduct(MSP())[indMSP()]))
} else NULL
}
})
output$annotationButton <- renderUI({
if (!is.null(msp)) {
if (length(indClick$ind) > 0 && onCircle$is)
actionButton(inputId = "annotate", label = "update annotation")
}
})
indMSP <- reactive({
if (length(indClick$ind) > 0) {
nameClick <- GN()[indClick$ind]
trNameClick <- truncateName(nameClick, roundDigits = NULL, group = TRUE)
which(trNameClick == groupname)
}
})
indMSPAnn <- eventReactive(input$annotate, {
indMSP()
})
## eventReactive for input$name
annotateNames <- eventReactive(input$annotate, {
as.character(input$names)
})
## eventReactive for input$classes
annotateClasses <- eventReactive(input$annotate, {
as.character(input$classes)
})
## eventReactive for input$information
annotateInformation <- eventReactive(input$annotate, {
as.character(input$information)
})
## eventReactive for input$adduct
annotateAdduct <- eventReactive(input$annotate, {
as.character(input$adduct)
})
if (!is.null(msp)) {
observe({
mspannotation$names[indMSPAnn()] <- annotateNames()
})
observe({
mspannotation$classes[indMSPAnn()] <- annotateClasses()
})
observe({
mspannotation$information[indMSPAnn()] <- annotateInformation()
})
observe({
mspannotation$adduct[indMSPAnn()] <- annotateAdduct()
})
}
## reactive expression for msp
MSP <- reactive({
if (!is.null(msp)) {
msp <- new("MSP", msp = msp@msp,
names = mspannotation$names,
classes = mspannotation$classes,
information = mspannotation$information,
adduct = mspannotation$adduct, mz = msp@mz, rt = msp@rt)
} else {msp <- NULL}
msp
})
## end annotation
## use predefined similarityMatrix
simMat <- reactive({
if (input$order == "mz") simMat <- simMatMZ
if (input$order == "retentionTime") simMat <- simMatRT
if (input$order == "clustering") simMat <- simMatClustering
simMat
})
## ordering of features, use predefined groupname object
GN <- reactive({
if (input$order == "mz") GN <- groupnameMZ
if (input$order == "retentionTime") GN <- groupnameRT
if (input$order == "clustering") GN <- groupnameClustering
GN
})
## get degree of features
degreeFeatures <- reactive({
if (input$order == "mz") degFeatures <- degreeFeaturesMZ
if (input$order == "retentionTime") degFeatures <- degreeFeaturesRT
if (input$order == "clustering") degFeatures <- degreeFeaturesClust
degFeatures
})
## calculateLink0Matrix
link0Matrix <- reactive({
#if (!is.null(input$order)) {
if (input$order == "mz") link0Mat <- link0MatMZ
if (input$order == "retentionTime") link0Mat <- link0MatRT
if (input$order == "clustering") link0Mat <- link0MatClustering
link0Mat
#}
})
## create reactive expression for LinkMatrix which is cut according to
## set radioButton (input$choiceLinks)
LinkMatrix_cut <- reactive(cutLinkMatrix(link0Matrix(),
type = input$choiceLinks))
## threshold linkMatrix_cut
LinkMatrix_threshold <- reactive(thresholdLinkMatrix(LinkMatrix_cut(),
input$threshold[1], input$threshold[2]))
## reactiveValues for click Coordinates
CoordinatesNewClick <- reactiveValues(X = 0, Y = 0)
CoordinatesOldClick <- reactiveValues(X = 0, Y = 0)
observe({
if (!is.null(input$circosClick$x)) {
CoordinatesNewClick$X <- input$circosClick$x
CoordinatesNewClick$Y <- input$circosClick$y
CoordinatesOldClick$X <- CoordinatesNewClick$X
CoordinatesOldClick$Y <- CoordinatesNewClick$Y
} else {
CoordinatesNewClick$X <- CoordinatesOldClick$X
CoordinatesNewClick$Y <- CoordinatesOldClick$Y
}
})
## is mouse over the track 1?
onCircle <- reactiveValues(is = NULL)
observe({
if (!is.null(CoordinatesNewClick$X)) {
.dist <- sqrt(CoordinatesOldClick$X^2 + CoordinatesOldClick$Y^2)
if (.dist >= 0.8 & .dist <= 1) {
onCircle$is <- TRUE
} else {
onCircle$is <- FALSE
}
} else onCircle$is <- FALSE
})
## Click: which is the current sector?
indClick <- reactiveValues(ind = NULL)
observe({
if (!is.null(input$circosClick$x))
indClick$ind <- minFragCart2Polar(input$circosClick$x,
input$circosClick$y, degreeFeatures())
})
## double click: which is the current sector?
CoordinatesNewDblClick <- reactiveValues(X = 0, Y = 0)
CoordinatesOldDblClick <- reactiveValues(X = 0, Y = 0)
observe({
if (!is.null(input$circosDblClick$x)) {
CoordinatesNewDblClick$X <- input$circosDblClick$x
CoordinatesNewDblClick$Y <- input$circosDblClick$y
CoordinatesOldDblClick$X <- CoordinatesNewDblClick$X
CoordinatesOldDblClick$Y <- CoordinatesNewDblClick$Y
} else {
CoordinatesNewDblClick$X <- CoordinatesOldDblClick$X
CoordinatesNewDblClick$Y <- CoordinatesOldDblClick$Y
}
})
## reactive value which stores double clicked indices (inds = storage,
## new = new indices)
indDblClick <- reactiveValues(ind = NULL, new = NULL)
observe({
if (!is.null(input$circosDblClick$x)) {
minInd <- minFragCart2Polar(input$circosDblClick$x,
input$circosDblClick$y,
degreeFeatures())
if (!is.na(minInd)) {
GNselect <- GN()[minInd]
selected <- strsplit(GNselect, split = "_")[[1]]
groupSelected <- selected[1]
nameSelected <- selected[3]
newNG <- paste(groupSelected, nameSelected, sep = "_")
indDblClick$new <- newNG ## write truncated name to indDblClick$new
} else indDblClick$new <- NULL
} #else indDblClick$new <- NULL
})
observe({
input$resetClickIndices
isolate(indDblClickMZ$ind <- NULL)
isolate(indDblClickRT$ind <- NULL)
isolate(indDblClickCluster$ind <- NULL)
isolate(indDblClick$new <- NULL)
isolate(onCircle$is <- FALSE)
isolate(indClick$ind <- NULL)
})
## reset indClick when changing radio button order
observe({
input$order
isolate(onCircle$is <- FALSE)
isolate(indClick$ind <- NULL)
})
## write double-clicked (truncated) names to indDblClickMZ, indDblClickRT,
## indDblClickCluster
indDblClickMZ <- reactiveValues(ind = NULL)
observe({
if (!is.null(input$circosDblClick$x)) {
if (!is.null(indDblClick$new)) {
newMZ <- paste(groupMZ, nameMZ, sep = "_")
newIndMZ <- match(indDblClick$new, newMZ)
if (isolate(newIndMZ %in% indDblClickMZ$ind)) {
indDblClickMZ$ind <- isolate(indDblClickMZ$ind[-which(newIndMZ == indDblClickMZ$ind)])
} else {indDblClickMZ$ind <- isolate(c(indDblClickMZ$ind, newIndMZ))}
}
}
})
indDblClickRT <- reactiveValues(ind = NULL)
observe({
if (!is.null(input$circosDblClick$x)) {
if (!is.null(indDblClick$new)) {
newRT <- paste(groupRT, nameRT, sep = "_")
newIndRT <- match(indDblClick$new, newRT)
if (isolate(newIndRT %in% indDblClickRT$ind)) {
indDblClickRT$ind <- isolate(indDblClickRT$ind[-which(newIndRT == indDblClickRT$ind)])
} else {indDblClickRT$ind <- isolate(c(indDblClickRT$ind, newIndRT))}
}
}
})
indDblClickCluster <- reactiveValues(ind = NULL)
observe({
if (!is.null(input$circosDblClick$x)) {
if(!is.null(indDblClick$new)) {
newCl <- paste(groupClustering, nameClustering, sep = "_")
newIndCl <- match(indDblClick$new, newCl)
if (isolate(newIndCl %in% indDblClickCluster$ind)) {
indDblClickCluster$ind <- isolate(indDblClickCluster$ind[-which(newIndCl == indDblClickCluster$ind)])
} else {indDblClickCluster$ind <- isolate(c(indDblClickCluster$ind, newIndCl))}
}
}
})
## plotting
initializePlot <- reactive({
circos.initialize(factor(GN()),
xlim = matrix(rep(c(0,1), dim(similarityMatrix)[1]), ncol = 2,
byrow = TRUE) )
circos.trackPlotRegion(GN(), ylim=c(0,1))
})
output$circos <- renderPlot({
initializePlot()
if (onCircle$is) {
if (input$order == "mz") {
replayPlot(PlotHighlightMZ)
highlight(groupnameMZ, c(indClick$ind, indDblClickMZ$ind),
LinkMatrix_threshold())
}
if (input$order == "retentionTime") {
replayPlot(PlotHighlightRT)
highlight(groupnameRT, c(indClick$ind, indDblClickRT$ind),
LinkMatrix_threshold())
}
if (input$order == "clustering") {
replayPlot(PlotHighlightCluster)
highlight(groupnameClustering, c(indClick$ind, indDblClickCluster$ind),
LinkMatrix_threshold())
}
} else { ## if not onCircle$is
if (length(indDblClickMZ$ind) > 0) {
if (input$order == "mz") {
replayPlot(PlotHighlightMZ)
highlight(groupnameMZ, c(indDblClickMZ$ind), LinkMatrix_threshold())
}
if (input$order == "retentionTime") {
replayPlot(PlotHighlightRT)
highlight(groupnameRT, c(indDblClickRT$ind), LinkMatrix_threshold())
}
if (input$order == "clustering") {
replayPlot(PlotHighlightCluster)
highlight(groupnameClustering, c(indDblClickCluster$ind), LinkMatrix_threshold())
}
} else {
if (input$order == "mz") {
replayPlot(PlotFilledMZ)
plotCircos(groupnameMZ, LinkMatrix_threshold(),
initialize=FALSE, featureNames = FALSE,
groupSector = FALSE, groupName = FALSE,
links = TRUE, highlight = FALSE)
}
if (input$order == "retentionTime") {
#replayPlot(PlotFilledRT)
replayPlot(PlotFilledRT)
plotCircos(groupnameRT, LinkMatrix_threshold(),
initialize=FALSE, featureNames = FALSE,
groupSector = FALSE, groupName = FALSE,
links = TRUE, highlight = FALSE)
}
if (input$order == "clustering") {
replayPlot(PlotFilledCluster)
plotCircos(groupnameClustering, LinkMatrix_threshold(),
initialize = FALSE, featureNames = FALSE,
groupSector = FALSE, groupName = FALSE,
links = TRUE, highlight = FALSE)
}
}
}
})
output$sized_plot <- renderUI({
plotOutput("circos",
dblclick = "circosDblClick",
click = "circosClick",
width = ifelse(is.null(input$innerWidth), 0, input$innerWidth*0.5*input$plotSize),
height = ifelse(is.null(input$innerWidth), 0, input$innerWidth*0.5*input$plotSize))
})
output$circosLegend <- renderPlot({
if (!is.null(input$legend)) if(input$legend)
circosLegend(groupnameRT, highlight = TRUE)
})
## show when Clicking the feature which connects to it
linkMatIndsClick <- reactive({
getLinkMatrixIndices(GN()[indClick$ind], LinkMatrix_threshold())
})
output$clickConnectedFeature <- renderUI({
if (!is.null(onCircle$is)) {
if (onCircle$is)
HTML(printInformationSelect(groupname = groupname,
msp = MSP(), ind = indMSP(), lMatInd = linkMatIndsClick(),
linkMatrixThreshold = LinkMatrix_threshold(),
similarityMatrix = similarityMatrix, roundDigits = input$precision))
}
})
output$dblClickFeature <- renderText({
if (length(indDblClickMZ$ind) > 0)
c("(permanently) selected features: ",
truncateName(groupnameMZ[indDblClickMZ$ind],
roundDigits = input$precision, group = TRUE)
)
else "no features (permanently) selected"
})
## on exit
observe({
if (input$stop == 0)
return()
else {
circos.clear()
selectedFeatures <- as.character(paste(
groupMZ[indDblClickMZ$ind], nameMZ[indDblClickMZ$ind],
sep="_"))
stopApp(
if (!is.null(msp)) {
list(msp = MSP(), selectedFeatures = selectedFeatures)
} else {selectedFeatures}
)
}
})
}
app <- list(ui = ui, server = server)
runApp(app)
}
## to do
## second simmat for neutral losses
#' @name printInformationSelect
#' @title Display information on connected features of selected features
#' @description Displays information on connected features of selected features.
#' @usage printInformationSelect(groupname, msp = NULL, ind,
#' lMatInd, linkMatrixThreshold, similarityMatrix, roundDigits = 2)
#' @param groupname \code{character} vector with groupname of selected feature,
#' vector containing "group" and "name" to display, that is
#' a unique identifier of the features, "group" and "name" have to be separated
#' by \code{"_"} where "group" is the first and "name" is the last element
#' @param msp \code{MSP}, an S4 object of class \code{MSP} for information about
#' the selected feature
#' @param ind \code{numeric}
#' @param lMatInd \code{numeric} indices of selected features
#' @param linkMatrixThreshold \code{matrix} that contains information of linked
#' features for given thresholds
#' @param similarityMatrix \code{matrix} that is used to get information on the
#' degree of similarity, \code{similarityMat} is an ordered version of a
#' similarity matrix, see \code{?createOrderedSimMat}
#' @param roundDigits \code{numeric}, how many digits should be displayed?
#' @details \code{printInformationSelect} is for internal use.
#' @return \code{character} that is in HTML format
#' @examples
#' data("idMSMStoMSP", package = "MetCirc")
#' data("binnedMSP", package = "MetCirc")
#' ## use only a selection
#' binnedMSP <- binnedMSP[c(1:20, 29:48, 113:132, 240:259),]
#' similarityMat <- createSimilarityMatrix(binnedMSP)
#' groupname <- rownames(similarityMat)
#' ## order similarityMat according to mz
#' simMat <- createOrderedSimMat(similarityMat, order = "mz")
#' groupnameMZ <- rownames(simMat)
#' linkMat_thr <- createLinkMatrix(simMat, 0.8, 1)
#' ind <- 2
#' indMZ <- which(groupname[ind] == truncateName(groupnameMZ, NULL, group = TRUE))
#' linkMatInds <- getLinkMatrixIndices(groupnameMZ[indMZ], linkMat_thr)
#' MetCirc:::printInformationSelect(groupname = groupname,
#' msp = NULL, ind = ind, lMatInd = linkMatInds,
#' linkMatrixThreshold = linkMat_thr,
#' similarityMatrix = similarityMat, roundDigits = 2)
#' @author Thomas Naake, \email{thomasnaake@@googlemail.com}
printInformationSelect <- function(groupname, msp = NULL,
ind, lMatInd, linkMatrixThreshold, similarityMatrix, roundDigits = 2) {
## truncate name of linkMatrixThreshold
lMatThr <- linkMatrixThreshold
if (is.null(msp)) {
## selected feature
selectedFeat <- groupname[ind]
if (length(lMatInd) >= 1) {
## get connected features
connect <- unique(as.vector(lMatThr[lMatInd, c("name1", "name2")]))
selectedFeat <- truncateName(selectedFeat, roundDigits, TRUE)
connect <- truncateName(connect, roundDigits, TRUE)
## remove selectedFeat from connect
if (selectedFeat %in% connect)
connect <- connect[-which(connect == selectedFeat)]
connect <- paste(connect, collapse = " <br/>")
return(paste(c(selectedFeat, "connects to", "<br/>", connect),
collapse = " "))
} else
return(paste(c(selectedFeat, "does not connect to any feature"),
collapse = " "))
} else { ## if !is.null(msp)
## clicked feature: create msp and get identifier
selectFeatMSP <- msp[ind]
selectFeat <- groupname[ind]
if (length(lMatInd) == 0) {
selectFeat <- truncateName(selectFeat, roundDigits = roundDigits,
group = TRUE)
return(paste0(selectFeat, " (", selectFeatMSP@names, ", ",
selectFeatMSP@information, ", ",
selectFeatMSP@classes, ",", selectFeatMSP@adduct, ") ",
"does not connect to any feature"))
} else {
## connected features: find
connect <- unique(as.vector(lMatThr[lMatInd, c("name1", "name2")]))
connect <- truncateName(connect, NULL, TRUE)
## remove duplicated hovFeat in connect
if (selectFeat %in% connect) connect <- connect[-which(connect == selectFeat)]
matchedInd <- match(connect, groupname)
connectMSP <- msp[matchedInd]
connChar <- character()
degreeSimilarity <- similarityMatrix[selectFeat, ]
for (i in 1:length(connect)) {
connectMSPI <- connectMSP[i]
connectI <- connect[i]
degreeSimilarityI <- round(degreeSimilarity[connectI],3)
degreeSimilarityI <- as.numeric(degreeSimilarityI)
connectI <- truncateName(connectI, roundDigits = roundDigits,
group = TRUE)
newFeat <- paste0(connectI, " (", degreeSimilarityI, ", ",
connectMSPI@names, ", ", connectMSPI@information, ", ",
connectMSPI@classes, ", ", connectMSPI@adduct, ")", "<br/>")
connChar <- c(connChar, newFeat)
}
connChar <- paste(connChar, collapse=" ")
selectFeat <- truncateName(selectFeat, roundDigits = roundDigits,
group = TRUE)
return(paste0(selectFeat, " (", selectFeatMSP@names, ", ",
selectFeatMSP@information, ", ",
selectFeatMSP@classes, ", ", selectFeatMSP@adduct, ") connects to ",
" <br/>", connChar))
}
}
}
PlantDefenseMetabolism/MetCirc documentation built on May 8, 2019, 2:52 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.
#' @import grDevices
#' @import graphics
#' @name shinyCircos
#' @title Interactive visualisation of similarity and navigation of MS/MS features
#' @description Visualise the similarity of MS/MS features in a reactive
#' context. See \code{Details} the vignette for further descriptions on how to use
#' \code{shinyCircos}.
#' @usage shinyCircos(similarityMatrix, msp = NULL, ...)
#' @param similarityMatrix \code{matrix}, \code{similarityMatrix} contains
#' pair-wise similarity coefficients which give information about the similarity
#' between MS/MS features
#' @param msp \code{MSP}, an S4 object of class \code{MSP}, the
#' \code{MSP}-object will be used to display information about the selected
#' feature
#' @param ... further arguments passed to \code{shinyCircos}, e.g.
#' \code{cexFeatureNames} to pass to \code{plotCircos} to set font size in
#' \code{plotCircos} of feature names
#' @details The function is based on the \code{shiny} and \code{circlize} package.
#' The user can choose interactively thresholds, type of links (between or
#' within groups), display information about MS/MS features, permanently select
#' MS/MS features and export selected precursors. When running
#' \code{shinyCircos} with the object of class \code{MSP}, annotation data of
#' selected MS/MS features will be displayed.
#' @return \code{shinyCircos} returns a \code{character} vector with the
#' (permanently) selected precursors or an object with the entries \code{msp}
#' and \code{selectedFeatures} if a \code{MSP}-object was passed to
#' \code{shinyCircos}
#' @author Thomas Naake, \email{thomasnaake@@googlemail.com}
#' @examples
#' data("idMSMStoMSP", package = "MetCirc")
#' ## truncate files
#' finalMSP <- finalMSP[c(1:20, 29:48, 113:132, 240:259)]
#' data("binnedMSP", package = "MetCirc")
#' binnedMSP <- binnedMSP[c(1:20, 29:48, 113:132, 240:259),]
#' similarityMat <- createSimilarityMatrix(binnedMSP)
#' \dontrun{shinyCircos(similarityMatrix = similarityMat, msp = finalMSP)}
#' @export
shinyCircos <- function(similarityMatrix, msp = NULL, ...) {
if (!is.null(msp)) if (class(msp) != "MSP") stop("msp is not of class MSP")
## circlize parameters
circos.par(gap.degree = 0, cell.padding = c(0, 0, 0, 0),
track.margin = c(0.0, 0))
groupname <- rownames(similarityMatrix)
## create plots and assign to objects by recordPlot
## rt
simMatRT <- createOrderedSimMat(similarityMatrix, order = "retentionTime")
link0MatRT <- createLink0Matrix(simMatRT)
groupnameRT <- rownames(simMatRT)
plotCircos(groupnameRT, NULL, initialize=TRUE, featureNames = TRUE,
groupSector = TRUE, groupName = FALSE, links = FALSE,
highlight = FALSE, ...)
PlotFilledRT <- recordPlot()
## get group and name from groupnameRT argument
## groupnameRT is a vector containing information about group and name,
## where group is the first element and name the last element separated by _
groupRT <- lapply(strsplit(groupnameRT, split = "_"), "[", 1)
groupRT <- unlist(groupRT)
nameRT <- lapply(strsplit(groupnameRT, split = "_"), function (x) x[length(x)])
nameRT <- unlist(nameRT)
## get degree of features
degreeFeaturesRT <- lapply(groupnameRT,
function(x) mean(circlize:::get.sector.data(x)[c("start.degree", "end.degree")]))
plot.new()
plotCircos(groupnameRT, NULL, initialize=TRUE, featureNames = TRUE,
groupSector = TRUE, groupName = FALSE, links = FALSE,
highlight = TRUE, ...)
PlotHighlightRT <- recordPlot()
plot.new()
## mz
simMatMZ <- createOrderedSimMat(similarityMatrix, order = "mz")
link0MatMZ <- createLink0Matrix(simMatMZ)
groupnameMZ <- rownames(simMatMZ)
plotCircos(groupnameMZ, NULL, initialize=TRUE, featureNames = TRUE,
groupSector = TRUE, groupName = FALSE, links = FALSE,
highlight = FALSE, ...)
PlotFilledMZ <- recordPlot()
## get group and name from groupnameMZ argument
## groupnameMZ is a vector containing information about group and name,
## where group is the first element and name the last element separated by _
groupMZ <- lapply(strsplit(groupnameMZ, split = "_"), "[", 1)
groupMZ <- unlist(groupMZ)
nameMZ <- lapply(strsplit(groupnameMZ, split = "_"), function (x) x[length(x)])
nameMZ <- unlist(nameMZ)
## get degree of features
degreeFeaturesMZ <- lapply(groupnameMZ,
function(x) mean(circlize:::get.sector.data(x)[c("start.degree", "end.degree")]))
plot.new()
plotCircos(groupnameMZ, NULL, initialize=TRUE, featureNames = TRUE,
groupSector = TRUE, groupName = FALSE, links = FALSE,
highlight = TRUE, ...)
PlotHighlightMZ <- recordPlot()
plot.new()
## clustering
simMatClustering <- createOrderedSimMat(similarityMatrix,
order = "clustering")
link0MatClustering <- createLink0Matrix(simMatClustering)
groupnameClustering <- rownames(simMatClustering)
plotCircos(groupnameClustering, NULL, initialize=TRUE,
featureNames = TRUE, groupSector = TRUE, groupName = FALSE,
links = FALSE, highlight = FALSE, ...)
PlotFilledCluster <- recordPlot()
## get group and name from groupnameMZ argument
## groupnameMZ is a vector containing information about group and name,
## where group is the first element and name the last element separated by _
groupClustering <- lapply(strsplit(groupnameClustering, split = "_"), "[", 1)
groupClustering <- unlist(groupClustering)
nameClustering <- lapply(strsplit(groupnameClustering, split = "_"),
function (x) x[length(x)])
nameClustering <- unlist(nameClustering)
## get degree of features
degreeFeaturesClust <- lapply(groupnameClustering,
function(x) mean(circlize:::get.sector.data(x)[c("start.degree", "end.degree")]))
plot.new()
plotCircos(groupnameClustering, NULL, initialize=TRUE, featureNames = TRUE,
groupSector = TRUE, groupName = FALSE, links = FALSE,
highlight = TRUE, ...)
PlotHighlightCluster <- recordPlot()
plot.new()
ui <- fluidPage(
tags$head(tags$script('
$(document).on("shiny:connected", function(e) {
Shiny.onInputChange("innerWidth", window.innerWidth);
});
$(window).resize(function(e) {
Shiny.onInputChange("innerWidth", window.innerWidth);
});
'
)),
column(4,
fluidRow(
tabsetPanel(id = "tabs",
tabPanel("Main", wellPanel(
radioButtons("choiceLinks", "choose type of links",
choices = c("all" = "all", "inter-class links" = "inter",
"intra-class links" = "intra"),
selected = "all"),
sliderInput("threshold",
"Threshold for similarity to display",
min = 0, max = 1, value = c(0.8, 1)),
radioButtons("order", "order within groups",
choices = c("clustering" = "clustering",
"m/z" = "mz", "retention time" = "retentionTime"),
selected = "mz"),
uiOutput("annotationName"),
uiOutput("annotationClass"),
uiOutput("annotationInformation"),
uiOutput("annotationAdduct"),
uiOutput("annotationButton"),
actionButton("resetClickIndices", "Reset features"),
actionButton("stop", "Stop and export \n selected features")
)),
tabPanel("Appearance", wellPanel(
sliderInput("plotSize", "plot size",
min = 0.5, max = 1.5, value = 1),
sliderInput("precision", "precision of numbers", value = 2, min = 0, max = 5, step = 1),
checkboxInput("legend", "legend", value = FALSE)
))
)
),
plotOutput("circosLegend", height = "300")
),
column(8,
fluidRow(uiOutput("sized_plot")),
fluidRow(
verbatimTextOutput("dimension_display"),
htmlOutput("clickConnectedFeature"),
verbatimTextOutput("dblClickFeature")
)
)
)
server <- function(input, output, session) {
## annotation
if(!is.null(msp)) {mspannotation <- reactiveValues(
names = msp@names, information = msp@information,
classes = msp@classes, adduct = msp@adduct)}
output$annotationName <- renderUI({
if (!is.null(msp)) {
if (length(indClick$ind) > 0 && onCircle$is) {
textInput("names", label = "name",
value = isolate(names(MSP())[indMSP()]))
} else NULL
}
})
output$annotationClass <- renderUI({
if (!is.null(msp)) {
if (length(indClick$ind) > 0 && onCircle$is) {
textInput("classes", label = "class",
value = isolate(classes(MSP())[indMSP()]))
} else NULL
}
})
output$annotationInformation <- renderUI({
if (!is.null(msp)) {
if (length(indClick$ind) > 0 && onCircle$is) {
#if (onCircle$is) {
textInput("information", label = "information",
value = isolate(information(MSP())[indMSP()]))
} else NULL
}
})
output$annotationAdduct <- renderUI({
if (!is.null(msp)) {
if (length(indClick$ind) > 0 && onCircle$is) {
textInput("adduct", label = "adduct",
value = isolate(adduct(MSP())[indMSP()]))
} else NULL
}
})
output$annotationButton <- renderUI({
if (!is.null(msp)) {
if (length(indClick$ind) > 0 && onCircle$is)
actionButton(inputId = "annotate", label = "update annotation")
}
})
indMSP <- reactive({
if (length(indClick$ind) > 0) {
nameClick <- GN()[indClick$ind]
trNameClick <- truncateName(nameClick, roundDigits = NULL, group = TRUE)
which(trNameClick == groupname)
}
})
indMSPAnn <- eventReactive(input$annotate, {
indMSP()
})
## eventReactive for input$name
annotateNames <- eventReactive(input$annotate, {
as.character(input$names)
})
## eventReactive for input$classes
annotateClasses <- eventReactive(input$annotate, {
as.character(input$classes)
})
## eventReactive for input$information
annotateInformation <- eventReactive(input$annotate, {
as.character(input$information)
})
## eventReactive for input$adduct
annotateAdduct <- eventReactive(input$annotate, {
as.character(input$adduct)
})
if (!is.null(msp)) {
observe({
mspannotation$names[indMSPAnn()] <- annotateNames()
})
observe({
mspannotation$classes[indMSPAnn()] <- annotateClasses()
})
observe({
mspannotation$information[indMSPAnn()] <- annotateInformation()
})
observe({
mspannotation$adduct[indMSPAnn()] <- annotateAdduct()
})
}
## reactive expression for msp
MSP <- reactive({
if (!is.null(msp)) {
msp <- new("MSP", msp = msp@msp,
names = mspannotation$names,
classes = mspannotation$classes,
information = mspannotation$information,
adduct = mspannotation$adduct, mz = msp@mz, rt = msp@rt)
} else {msp <- NULL}
msp
})
## end annotation
## use predefined similarityMatrix
simMat <- reactive({
if (input$order == "mz") simMat <- simMatMZ
if (input$order == "retentionTime") simMat <- simMatRT
if (input$order == "clustering") simMat <- simMatClustering
simMat
})
## ordering of features, use predefined groupname object
GN <- reactive({
if (input$order == "mz") GN <- groupnameMZ
if (input$order == "retentionTime") GN <- groupnameRT
if (input$order == "clustering") GN <- groupnameClustering
GN
})
## get degree of features
degreeFeatures <- reactive({
if (input$order == "mz") degFeatures <- degreeFeaturesMZ
if (input$order == "retentionTime") degFeatures <- degreeFeaturesRT
if (input$order == "clustering") degFeatures <- degreeFeaturesClust
degFeatures
})
## calculateLink0Matrix
link0Matrix <- reactive({
#if (!is.null(input$order)) {
if (input$order == "mz") link0Mat <- link0MatMZ
if (input$order == "retentionTime") link0Mat <- link0MatRT
if (input$order == "clustering") link0Mat <- link0MatClustering
link0Mat
#}
})
## create reactive expression for LinkMatrix which is cut according to
## set radioButton (input$choiceLinks)
LinkMatrix_cut <- reactive(cutLinkMatrix(link0Matrix(),
type = input$choiceLinks))
## threshold linkMatrix_cut
LinkMatrix_threshold <- reactive(thresholdLinkMatrix(LinkMatrix_cut(),
input$threshold[1], input$threshold[2]))
## reactiveValues for click Coordinates
CoordinatesNewClick <- reactiveValues(X = 0, Y = 0)
CoordinatesOldClick <- reactiveValues(X = 0, Y = 0)
observe({
if (!is.null(input$circosClick$x)) {
CoordinatesNewClick$X <- input$circosClick$x
CoordinatesNewClick$Y <- input$circosClick$y
CoordinatesOldClick$X <- CoordinatesNewClick$X
CoordinatesOldClick$Y <- CoordinatesNewClick$Y
} else {
CoordinatesNewClick$X <- CoordinatesOldClick$X
CoordinatesNewClick$Y <- CoordinatesOldClick$Y
}
})
## is mouse over the track 1?
onCircle <- reactiveValues(is = NULL)
observe({
if (!is.null(CoordinatesNewClick$X)) {
.dist <- sqrt(CoordinatesOldClick$X^2 + CoordinatesOldClick$Y^2)
if (.dist >= 0.8 & .dist <= 1) {
onCircle$is <- TRUE
} else {
onCircle$is <- FALSE
}
} else onCircle$is <- FALSE
})
## Click: which is the current sector?
indClick <- reactiveValues(ind = NULL)
observe({
if (!is.null(input$circosClick$x))
indClick$ind <- minFragCart2Polar(input$circosClick$x,
input$circosClick$y, degreeFeatures())
})
## double click: which is the current sector?
CoordinatesNewDblClick <- reactiveValues(X = 0, Y = 0)
CoordinatesOldDblClick <- reactiveValues(X = 0, Y = 0)
observe({
if (!is.null(input$circosDblClick$x)) {
CoordinatesNewDblClick$X <- input$circosDblClick$x
CoordinatesNewDblClick$Y <- input$circosDblClick$y
CoordinatesOldDblClick$X <- CoordinatesNewDblClick$X
CoordinatesOldDblClick$Y <- CoordinatesNewDblClick$Y
} else {
CoordinatesNewDblClick$X <- CoordinatesOldDblClick$X
CoordinatesNewDblClick$Y <- CoordinatesOldDblClick$Y
}
})
## reactive value which stores double clicked indices (inds = storage,
## new = new indices)
indDblClick <- reactiveValues(ind = NULL, new = NULL)
observe({
if (!is.null(input$circosDblClick$x)) {
minInd <- minFragCart2Polar(input$circosDblClick$x,
input$circosDblClick$y,
degreeFeatures())
if (!is.na(minInd)) {
GNselect <- GN()[minInd]
selected <- strsplit(GNselect, split = "_")[[1]]
groupSelected <- selected[1]
nameSelected <- selected[3]
newNG <- paste(groupSelected, nameSelected, sep = "_")
indDblClick$new <- newNG ## write truncated name to indDblClick$new
} else indDblClick$new <- NULL
} #else indDblClick$new <- NULL
})
observe({
input$resetClickIndices
isolate(indDblClickMZ$ind <- NULL)
isolate(indDblClickRT$ind <- NULL)
isolate(indDblClickCluster$ind <- NULL)
isolate(indDblClick$new <- NULL)
isolate(onCircle$is <- FALSE)
isolate(indClick$ind <- NULL)
})
## reset indClick when changing radio button order
observe({
input$order
isolate(onCircle$is <- FALSE)
isolate(indClick$ind <- NULL)
})
## write double-clicked (truncated) names to indDblClickMZ, indDblClickRT,
## indDblClickCluster
indDblClickMZ <- reactiveValues(ind = NULL)
observe({
if (!is.null(input$circosDblClick$x)) {
if (!is.null(indDblClick$new)) {
newMZ <- paste(groupMZ, nameMZ, sep = "_")
newIndMZ <- match(indDblClick$new, newMZ)
if (isolate(newIndMZ %in% indDblClickMZ$ind)) {
indDblClickMZ$ind <- isolate(indDblClickMZ$ind[-which(newIndMZ == indDblClickMZ$ind)])
} else {indDblClickMZ$ind <- isolate(c(indDblClickMZ$ind, newIndMZ))}
}
}
})
indDblClickRT <- reactiveValues(ind = NULL)
observe({
if (!is.null(input$circosDblClick$x)) {
if (!is.null(indDblClick$new)) {
newRT <- paste(groupRT, nameRT, sep = "_")
newIndRT <- match(indDblClick$new, newRT)
if (isolate(newIndRT %in% indDblClickRT$ind)) {
indDblClickRT$ind <- isolate(indDblClickRT$ind[-which(newIndRT == indDblClickRT$ind)])
} else {indDblClickRT$ind <- isolate(c(indDblClickRT$ind, newIndRT))}
}
}
})
indDblClickCluster <- reactiveValues(ind = NULL)
observe({
if (!is.null(input$circosDblClick$x)) {
if(!is.null(indDblClick$new)) {
newCl <- paste(groupClustering, nameClustering, sep = "_")
newIndCl <- match(indDblClick$new, newCl)
if (isolate(newIndCl %in% indDblClickCluster$ind)) {
indDblClickCluster$ind <- isolate(indDblClickCluster$ind[-which(newIndCl == indDblClickCluster$ind)])
} else {indDblClickCluster$ind <- isolate(c(indDblClickCluster$ind, newIndCl))}
}
}
})
## plotting
initializePlot <- reactive({
circos.initialize(factor(GN()),
xlim = matrix(rep(c(0,1), dim(similarityMatrix)[1]), ncol = 2,
byrow = TRUE) )
circos.trackPlotRegion(GN(), ylim=c(0,1))
})
output$circos <- renderPlot({
initializePlot()
if (onCircle$is) {
if (input$order == "mz") {
replayPlot(PlotHighlightMZ)
highlight(groupnameMZ, c(indClick$ind, indDblClickMZ$ind),
LinkMatrix_threshold())
}
if (input$order == "retentionTime") {
replayPlot(PlotHighlightRT)
highlight(groupnameRT, c(indClick$ind, indDblClickRT$ind),
LinkMatrix_threshold())
}
if (input$order == "clustering") {
replayPlot(PlotHighlightCluster)
highlight(groupnameClustering, c(indClick$ind, indDblClickCluster$ind),
LinkMatrix_threshold())
}
} else { ## if not onCircle$is
if (length(indDblClickMZ$ind) > 0) {
if (input$order == "mz") {
replayPlot(PlotHighlightMZ)
highlight(groupnameMZ, c(indDblClickMZ$ind), LinkMatrix_threshold())
}
if (input$order == "retentionTime") {
replayPlot(PlotHighlightRT)
highlight(groupnameRT, c(indDblClickRT$ind), LinkMatrix_threshold())
}
if (input$order == "clustering") {
replayPlot(PlotHighlightCluster)
highlight(groupnameClustering, c(indDblClickCluster$ind), LinkMatrix_threshold())
}
} else {
if (input$order == "mz") {
replayPlot(PlotFilledMZ)
plotCircos(groupnameMZ, LinkMatrix_threshold(),
initialize=FALSE, featureNames = FALSE,
groupSector = FALSE, groupName = FALSE,
links = TRUE, highlight = FALSE)
}
if (input$order == "retentionTime") {
#replayPlot(PlotFilledRT)
replayPlot(PlotFilledRT)
plotCircos(groupnameRT, LinkMatrix_threshold(),
initialize=FALSE, featureNames = FALSE,
groupSector = FALSE, groupName = FALSE,
links = TRUE, highlight = FALSE)
}
if (input$order == "clustering") {
replayPlot(PlotFilledCluster)
plotCircos(groupnameClustering, LinkMatrix_threshold(),
initialize = FALSE, featureNames = FALSE,
groupSector = FALSE, groupName = FALSE,
links = TRUE, highlight = FALSE)
}
}
}
})
output$sized_plot <- renderUI({
plotOutput("circos",
dblclick = "circosDblClick",
click = "circosClick",
width = ifelse(is.null(input$innerWidth), 0, input$innerWidth*0.5*input$plotSize),
height = ifelse(is.null(input$innerWidth), 0, input$innerWidth*0.5*input$plotSize))
})
output$circosLegend <- renderPlot({
if (!is.null(input$legend)) if(input$legend)
circosLegend(groupnameRT, highlight = TRUE)
})
## show when Clicking the feature which connects to it
linkMatIndsClick <- reactive({
getLinkMatrixIndices(GN()[indClick$ind], LinkMatrix_threshold())
})
output$clickConnectedFeature <- renderUI({
if (!is.null(onCircle$is)) {
if (onCircle$is)
HTML(printInformationSelect(groupname = groupname,
msp = MSP(), ind = indMSP(), lMatInd = linkMatIndsClick(),
linkMatrixThreshold = LinkMatrix_threshold(),
similarityMatrix = similarityMatrix, roundDigits = input$precision))
}
})
output$dblClickFeature <- renderText({
if (length(indDblClickMZ$ind) > 0)
c("(permanently) selected features: ",
truncateName(groupnameMZ[indDblClickMZ$ind],
roundDigits = input$precision, group = TRUE)
)
else "no features (permanently) selected"
})
## on exit
observe({
if (input$stop == 0)
return()
else {
circos.clear()
selectedFeatures <- as.character(paste(
groupMZ[indDblClickMZ$ind], nameMZ[indDblClickMZ$ind],
sep="_"))
stopApp(
if (!is.null(msp)) {
list(msp = MSP(), selectedFeatures = selectedFeatures)
} else {selectedFeatures}
)
}
})
}
app <- list(ui = ui, server = server)
runApp(app)
}
## to do
## second simmat for neutral losses
#' @name printInformationSelect
#' @title Display information on connected features of selected features
#' @description Displays information on connected features of selected features.
#' @usage printInformationSelect(groupname, msp = NULL, ind,
#' lMatInd, linkMatrixThreshold, similarityMatrix, roundDigits = 2)
#' @param groupname \code{character} vector with groupname of selected feature,
#' vector containing "group" and "name" to display, that is
#' a unique identifier of the features, "group" and "name" have to be separated
#' by \code{"_"} where "group" is the first and "name" is the last element
#' @param msp \code{MSP}, an S4 object of class \code{MSP} for information about
#' the selected feature
#' @param ind \code{numeric}
#' @param lMatInd \code{numeric} indices of selected features
#' @param linkMatrixThreshold \code{matrix} that contains information of linked
#' features for given thresholds
#' @param similarityMatrix \code{matrix} that is used to get information on the
#' degree of similarity, \code{similarityMat} is an ordered version of a
#' similarity matrix, see \code{?createOrderedSimMat}
#' @param roundDigits \code{numeric}, how many digits should be displayed?
#' @details \code{printInformationSelect} is for internal use.
#' @return \code{character} that is in HTML format
#' @examples
#' data("idMSMStoMSP", package = "MetCirc")
#' data("binnedMSP", package = "MetCirc")
#' ## use only a selection
#' binnedMSP <- binnedMSP[c(1:20, 29:48, 113:132, 240:259),]
#' similarityMat <- createSimilarityMatrix(binnedMSP)
#' groupname <- rownames(similarityMat)
#' ## order similarityMat according to mz
#' simMat <- createOrderedSimMat(similarityMat, order = "mz")
#' groupnameMZ <- rownames(simMat)
#' linkMat_thr <- createLinkMatrix(simMat, 0.8, 1)
#' ind <- 2
#' indMZ <- which(groupname[ind] == truncateName(groupnameMZ, NULL, group = TRUE))
#' linkMatInds <- getLinkMatrixIndices(groupnameMZ[indMZ], linkMat_thr)
#' MetCirc:::printInformationSelect(groupname = groupname,
#' msp = NULL, ind = ind, lMatInd = linkMatInds,
#' linkMatrixThreshold = linkMat_thr,
#' similarityMatrix = similarityMat, roundDigits = 2)
#' @author Thomas Naake, \email{thomasnaake@@googlemail.com}
printInformationSelect <- function(groupname, msp = NULL,
ind, lMatInd, linkMatrixThreshold, similarityMatrix, roundDigits = 2) {
## truncate name of linkMatrixThreshold
lMatThr <- linkMatrixThreshold
if (is.null(msp)) {
## selected feature
selectedFeat <- groupname[ind]
if (length(lMatInd) >= 1) {
## get connected features
connect <- unique(as.vector(lMatThr[lMatInd, c("name1", "name2")]))
selectedFeat <- truncateName(selectedFeat, roundDigits, TRUE)
connect <- truncateName(connect, roundDigits, TRUE)
## remove selectedFeat from connect
if (selectedFeat %in% connect)
connect <- connect[-which(connect == selectedFeat)]
connect <- paste(connect, collapse = " <br/>")
return(paste(c(selectedFeat, "connects to", "<br/>", connect),
collapse = " "))
} else
return(paste(c(selectedFeat, "does not connect to any feature"),
collapse = " "))
} else { ## if !is.null(msp)
## clicked feature: create msp and get identifier
selectFeatMSP <- msp[ind]
selectFeat <- groupname[ind]
if (length(lMatInd) == 0) {
selectFeat <- truncateName(selectFeat, roundDigits = roundDigits,
group = TRUE)
return(paste0(selectFeat, " (", selectFeatMSP@names, ", ",
selectFeatMSP@information, ", ",
selectFeatMSP@classes, ",", selectFeatMSP@adduct, ") ",
"does not connect to any feature"))
} else {
## connected features: find
connect <- unique(as.vector(lMatThr[lMatInd, c("name1", "name2")]))
connect <- truncateName(connect, NULL, TRUE)
## remove duplicated hovFeat in connect
if (selectFeat %in% connect) connect <- connect[-which(connect == selectFeat)]
matchedInd <- match(connect, groupname)
connectMSP <- msp[matchedInd]
connChar <- character()
degreeSimilarity <- similarityMatrix[selectFeat, ]
for (i in 1:length(connect)) {
connectMSPI <- connectMSP[i]
connectI <- connect[i]
degreeSimilarityI <- round(degreeSimilarity[connectI],3)
degreeSimilarityI <- as.numeric(degreeSimilarityI)
connectI <- truncateName(connectI, roundDigits = roundDigits,
group = TRUE)
newFeat <- paste0(connectI, " (", degreeSimilarityI, ", ",
connectMSPI@names, ", ", connectMSPI@information, ", ",
connectMSPI@classes, ", ", connectMSPI@adduct, ")", "<br/>")
connChar <- c(connChar, newFeat)
}
connChar <- paste(connChar, collapse=" ")
selectFeat <- truncateName(selectFeat, roundDigits = roundDigits,
group = TRUE)
return(paste0(selectFeat, " (", selectFeatMSP@names, ", ",
selectFeatMSP@information, ", ",
selectFeatMSP@classes, ", ", selectFeatMSP@adduct, ") connects to ",
" <br/>", connChar))
}
}
}
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.