#' figure2
#'
#' @param mzPointer mzR object
#' @param pol polarity
#'
#' @return plotly plot
#' @export
#'
figure2 <- function(mzPointer,
pol) {
mzXMLHeader <- mzPlotter::readMzSpec(mzPointer)
mzXMLHeader <- mzXMLHeader[mzXMLHeader$msLevel == 2, ]
mzXMLHeader <- mzXMLHeader[mzXMLHeader$polarity == pol, ]
maxTic <- max(getTic(mzHeader = mzXMLHeader))
maxBpc <- max(getBpc(mzHeader = mzXMLHeader))
relInt <- mzPlotter::relativateTotalAndBase(maxTic = maxTic,
maxBpc = maxBpc)
mzXMLHeader$relInt <- relInt
mzXMLHeader$retentionTime <- base::round(mzXMLHeader$retentionTime / 60,
2)
mzXMLHeader$totIonCurrent <- round((mzXMLHeader$totIonCurrent / max(mzXMLHeader$totIonCurrent)) * 100,
2)
mzXMLHeader$scaledBasePeakIntensity <- log10(mzXMLHeader$basePeakIntensity + 1)
mzXMLHeader$scaledTotIonCurrent <- log10(mzXMLHeader$totIonCurrent + 1)
mzXMLHeader$basePeakIntensity <- -round((mzXMLHeader$basePeakIntensity / max(mzXMLHeader$basePeakIntensity)) * 100,
2)
sd_2 <- crosstalk::SharedData$new(mzXMLHeader, key = ~acquisitionNum, group = "mzXMLHeader_subset")
plotly::subplot(
nrows = 2,
shareX = F,
shareY = F,
titleX = T,
titleY = T,
margin = 0.08,
plotly::highlight(plotly::ggplotly(ticBpcPlot(sd_2),
tooltip = c("label1", "label2")),
on = "plotly_selected",
color = "red"),
plotly::subplot(
nrows = 1,
shareX = F,
shareY = F,
titleX = T,
titleY = T,
margin = 0.08,
plotly::highlight(plotly::ggplotly(precEvalMs2Plot(sd_2),
tooltip = c("label1", "label2")),
on = "plotly_selected",
color = "red"),
plotly::highlight(plotly::ggplotly(rtVsPrecMzPlot(sd_2),
tooltip = c("label1", "label2")),
on = "plotly_selected",
color = "red")
))
}
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