R/plotting-dataframe.R

In MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics

plot2d.header <- function(object, ## MSnExp header
                          z = c("ionCount", "file", "peaks.count", "charge"),
                          alpha,
                          plot) {
  z <- match.arg(z)
  stopifnot(c("retention.time","precursor.mz", z) %in% names(object))
  peaks.count <- charge <- retention.time <- precursor.mz <- NULL # to satisfy codetools
  p <- ggplot(object, aes(retention.time,precursor.mz)) + labs(colour = z)
  switch(z,
         ionCount = p <- p + geom_point(aes(colour=ionCount), alpha=alpha),
         peaks.count = p <- p + geom_point(aes(colour=peaks.count), alpha=alpha),
         file = p <- p + geom_point(aes(colour=as.factor(file)), alpha=alpha),
         charge = p <- p + geom_point(aes(colour=as.factor(charge)), alpha=alpha))
  if (plot)
    print(p)
  invisible(p)
}

plotDensity.header <- function(object, ## MSnExp header
                               z = c("precursor.mz", "peaks.count", "ionCount"),
                               log,
                               plot) {
    z <- match.arg(z)
    stopifnot(z %in% names(object))
    peaks.count <- charge <- ionCount <- precursor.mz <- NULL # to satisfy codetools
    object$charge <- as.factor(object$charge)
    switch(z,
           precursor.mz = p <- ggplot(object, aes(precursor.mz)) + xlab("Precursor M/Z"),
           peaks.count = p <- ggplot(object, aes(peaks.count)) + xlab("Peaks count"),
           ionCount = p <- ggplot(object, aes(ionCount)) + xlab("Total ion current"))
    if ("charge" %in% names(object))
        p <- p + geom_freqpoly(aes(group = charge,
                                   colour = charge))
    if (log)
        p <- p + scale_x_log10()
    if (plot)
        print(p)
    invisible(p)
}