R/figure2.R

In chasemc/mzPlotter:

#' 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")
    ))

}