tag.spectra.butterflyplot {protag}

tag.spectra.butterflyplot

Description

This function takes the output dataset from tag.search, and draw using ggplot2 the centroid mass spectra displayed in a mirrored or "butterfly" 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.butterflyplot(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 = TRUE, 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 = 0.1,
  gap.annotation = 0.05)

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.

Details

Though similar to tag.spectra.listplot, tag.spectra.butterflyplot is specifically designed for comparison of TWO mass spectra with the highest annotation clarity. That is, the “group” variable of the associated feeding dataset should contain only two unique levels, “control” and another named level. In case of existence of more than two levels in the “group” variable, all levels except “control” will be plotted overlapped with tag.spectra.butterflyplot; and it is recommended to use tag.spectra.listplot instead for multiple spectra drawing.

Value

a ggplot2 plot.

Examples

subset <-  myoglobin[myoglobin$group %in% c("control", "label1"), ]
search.result <- tag.search(subset, delta = c(14, 28), error.Da.pair = .3)
tag.spectra.butterflyplot(search.result)