wrTopDownFrag (version 1.0.4)

plotNTheor: Plot the number of theoretical random fragments

Description

This simple function allows plotting the expected number of theoretical fragments from random fragmentation of peptides/proteins (in mass spectrometry). Here, only the pure fragmentation without any variable fragmentation is considered, all fragment-sizes are included (ie, no gating). For simplicity, possible (variable) modifications like loss of neutrals, etc, are not considered.

Usage

plotNTheor(
  x,
  tit = "Number of term and intern fragm",
  xlab = "Number of aa",
  ylab = "",
  col = 2:3,
  log = "",
  mark = NULL,
  cexMark = 0.75
)

Value

figure only

Arguments

x

(integer) length (in amino-acids) of input peptides/proteins to be considered

tit

(character) custom title

xlab

(character) custom x-axis label

ylab

(character) custom y-axis label

col

(character or integer) cutsom colors

log

(character) define which axis should be log (use "xy" for drawing both x- and y-axis as log-scale)

mark

(matrix) first column for text and second column for where it should be stated along the top border of the figure (x-coordinate)

cexMark

(numeric) cex expansion-factor for text from argument mark

See Also

AAfragSettings

Examples

marks <- data.frame(name=c("Ubiquitin\n76aa", "Glutamate dehydrogenase 1\n501aa"),
  length=c(76,501))
plotNTheor(x=20:750, log="", mark=marks)