tag.spectra.listplot: tag.spectra.listplot

In protag: Search Tagged Peptides & Draw Highlighted Mass Spectra

Description

This function takes the output dataset from tag.search, and draw using ggplot2 the centroid mass spectra displayed in a listed manner. Peaks from the same "pair" (with designated m/z difference) are highlighted in differentiating colors, distinguished away from peaks of the "match" (with the same m/z) and the "mismatch" (neither of the prior two cases).

Usage

tag.spectra.listplot(search.output.list, show.peak.pair = TRUE,
  show.peak.match = TRUE, show.peak.mismatch = TRUE,
  show.annotation.pair = TRUE, show.annotation.match = TRUE,
  show.annotation.mismatch = FALSE, size.peak.pair = 2,
  size.peak.match = 1, size.peak.mismatch = 0.5, size.divider = 0.3,
  size.annotation.pair = NA, size.annotation.match = NA,
  size.annotation.mismatch = NA, size.groupname = NA,
  alpha.peak.pair = 0.8, alpha.peak.match = 0.5,
  alpha.peak.mismatch = 0.2, alpha.annotation.pair = 0.8,
  alpha.annotation.match = 0.5, alpha.annotation.mismatch = 0.2,
  color.pair = 1, color.match = "black", color.mismatch = "black",
  color.groupname = "black", color.divider = "black",
  angle.annotation = 90, angle.groupname = 90, gap.groupname = 0.02,
  gap.annotation = 0.15, peak.height.shrink = 0.7)

Arguments

search.output.list	the output list from function tag.search
show.peak.pair	if TRUE, show the paired peaks
show.peak.match	if TRUE, show the matched peaks
show.peak.mismatch	if TRUE, show the mismatched peaks
show.annotation.pair	if TRUE, show the m/z annotations for the paired peaks
show.annotation.match	if TRUE, show the m/z annotations for the mathced peaks
show.annotation.mismatch	if TRUE, show the m/z annotations for the mismatched peaks
size.peak.pair	adjust the peak width of the paired peaks. All size.xxx arguments take a numeric value, same functionality as line width or text size control in ggplot2
size.peak.match	adjust the peak width of the matched peaks
size.peak.mismatch	adjust the peak width of the mismatched peaks
size.divider	adjust divider width
size.annotation.pair	adjust the m/z annotation text size for the paired peaks
size.annotation.match	adjust the m/z annotation text size for the matched peaks
size.annotation.mismatch	adjust the m/z annotation text size for the mismatched peaks
size.groupname	adjust the text size for groupnames (e.g., "control", "experiment1", "experiment2", etc.).
alpha.peak.pair	adjust the transparency of the paired peaks. All alpha.xxx arguments take a numeric value [0,1]
alpha.peak.match	adjust the transparency of the matched peaks
alpha.peak.mismatch	adjust the transparency of the mismatched peaks
alpha.annotation.pair	adjust the transparency of the m/z annotations for the paired peaks
alpha.annotation.match	adjust the transparency of the m/z annotations for the matched peaks
alpha.annotation.mismatch	adjust the transparency of the m/z annotations for the mismatched peaks
color.pair	control the color for the paired peaks and the associated m/z annotations. Each pair will be of the same color, and different pairs of differentiating colors. In case of multiple mass shifts being of interest within a pair, e.g., delta = c(14, 28, 56), then peaks with m/z difference of either 14, 28 or 56, all belonging to the same pair, will be of the same color. Apart from the default color set, users could otherwise choose color from RColorBrewer palettes, e.g., color.pair = "Set1", or color.pair = "Blues". Colors for peaks (paired, matched, and mismatched) and the respectively associated annotations are designed to be of the same set of color for maximum clarity.
color.match	control the color for the matched peaks with the associated m/z annotations, with default in "black". Users may otherwise reset to different colors, e.g., color.match = "firebrick". As the matched peaks and mismatched peaks are usually of less research interest than paired peaks, the matched and mismatched peaks are respectively designed to be of monocolor.
color.mismatch	control the color for the mismatched peaks with the associated m/z annotations, with default in "black".
color.groupname	control the color for the groupnames, with default in "black".
color.divider	control the color of the central divider
angle.annotation	adjust the angle for the m/z annotations, taking a numeric value. This argument is useful to avoid annotation overlap, and is particularly handy when the plot is reoriented with coord_flip().
angle.groupname	adjust the angle of the groupnames.
gap.groupname	adjust the horizontal position of groupnames. A positive numeric value adjusts the distance between groupnames and the left bound of the mass spectra; negative values shifts the groupnames to the right side.
gap.annotation	adjust the distance between m/z annotations and the top of the peak.
peak.height.shrink	Taking a numeric value [0, 1], a small shrinking factor renders smaller peak height, and generates more space between peak and the central divider, leaving more space for annotations. This argument resolves overlap among annotations with upper-floor-residing peaks, a problem unique to listplot. Therefore, this argument is not used in the butterflyplot.

Details

This function is designed for comparison of multiple mass spectra. In case of comparison of two mass spectra, it is recommended to use tag.spectra.butterflyplot for the highest annotation clarity.

Value

a ggplot2 plot.

Examples

search.result <- tag.search(myoglobin, delta = c(14, 28), error.Da.pair = .3)
search.result
tag.spectra.listplot(search.result)

protag documentation built on Aug. 9, 2019, 5:07 p.m.