plotFragmLoc: Plot Identified Fragments Relative To Their Location

In wrTopDownFrag: Internal Fragment Identification from Top-Down Mass Spectrometry

Plot Identified Fragments Relative To Their Location

Description

Take result from fragIonMass and display identified fragments by their location, an additional parameter (default logIntensity) is used for coloring This function illustrates the distribution of identfied peptidesa and thus common break-points.

Usage

plotFragmLoc(
  fraL,
  extrCol = NULL,
  useLog = FALSE,
  useCol = NULL,
  specLayout = NULL,
  useTi = NULL,
  subTit = NULL,
  footer = NULL,
  batchFig = FALSE,
  legCex = 0.5,
  legOffS = NULL,
  legBorder = NULL,
  silent = FALSE,
  callFrom = NULL,
  debug = FALSE
)

Arguments

fraL	(list) result from fragIonMass, must conatain elements ”
extrCol	(character) 1st should be aa seq of initial proteins (used for dimensionong graph and separating multiple input proteins), 2nd & 3rd start- and ed-site for drawing;, 4th the column to use for coloring), 5th for protein name in title of figure
useLog	(logical) take values for coloring (4th element of 'extrCol') as log10
useCol	(character) custom colors
specLayout	(character) custom layout
useTi	(character) custom title
subTit	(character) custom sub-title
footer	(character) custom footer
batchFig	(logical) reduce text content for multiple figues on page
legCex	(numeric, length=1) expansion factor
legOffS	(numeric) legend-offset (passed to legendHist)
legBorder	(logical) legend-border (passed to legendHist)
silent	(logical) suppress messages
callFrom	(character) allow easier tracking of message(s) produced
debug	(logical) additional messages for debugging

Value

This function returns a figure

See Also

identifFixedModif

Examples

protP <- c(protP="PEPTIDE")
obsMassX <- cbind(a=c(199.1077, 296.1605, 397.2082, 510.2922,625.3192),
  b=c(227.1026, 324.1554, 425.2031, 538.2871, 653.3141),
  x=c(729.2937, 600.2511, 503.1984, 402.1507, 289.0666),
  y=c(703.3145, 574.2719, 477.2191, 376.1714, 263.0874))
rownames(obsMassX) <- c("E","P","T","I","D")      # all 1 & 7 ions not included
identP1 <- identifFixedModif(prot=protP,expMass=as.numeric(obsMassX), minFragSize=2, 
  maxFragSize=7, modTy=list(basMod=c("b","y")))     #

wrTopDownFrag documentation built on June 8, 2025, 1:34 p.m.