wrTopDownFrag (version 1.0.4)

plotFragmLoc: 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
)

Value

This function returns a figure

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

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")))     #