protPlotfun: Plot profiles of reference proteins

In mooredf22/protlocassign0p1p1: Compute constrained proportional assignments for fractionated protein abundance

Description

This function plots the average profiles of any protein in the dataset, the peptide profiles, and also the reference profile for each compartment

Usage

protPlotfun(
  protName,
  profile,
  finalList = NULL,
  numDataCols = 9,
  n.compartments = 8,
  refLocationProfiles,
  assignPropsMat,
  transType = "",
  yAxisLabel = ""
)

Arguments

protName	Name of the protein to plot
profile	Data frame of protein names and their relative abundance levels..
finalList	spectrum-level abundance levels by protein and peptide; Ehis is NULL if not available
numDataCols	number of fractions per protein
n.compartments	number of compartments (8 in Jadot data)
refLocationProfiles	A matrix refLocationProfiles giving the abundance level profiles of the subcellular locations n.compartments = 8 columns are subcellular locations, and numDataCols rows are the fraction names
assignPropsMat	A matrix of assignment proportions for proteins of interest, from the constrained proportional assignment algorithm, and optionally upper and lower 95 percent confidence limits. Can be a single protein
transType	type of transformation (for plot label)
yAxisLabel	label for y-axis if present

Value

plot of protein, peptide, and reference profiles

Examples

data(protNSA_markerTLN1)
data(markerListJadot)
refLocationProfilesNSA <- locationProfileSetup(profile=protNSA_markerTLN1, markerList=markerListJadot, numDataCols=9)
protCPAfromNSA_test <- fitCPA(profile=protNSA_markerTLN1,
                              refLocationProfiles=refLocationProfilesNSA,
                              numDataCols=9)
protPlotfun(protName="TLN1", profile=protNSA_markerTLN1,
            numDataCols=9, n.compartments=8,
            refLocationProfiles=refLocationProfilesNSA,
            assignPropsMat=protCPAfromNSA_test,
            yAxisLabel="Normalized Specific Amount")

mooredf22/protlocassign0p1p1 documentation built on Feb. 7, 2022, 1:55 a.m.