protPepPlotfun: 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

protPepPlotfun(
  protName,
  protProfile,
  Nspectra = TRUE,
  pepProfile = NULL,
  numRefCols,
  numDataCols,
  n.compartments = 8,
  refLocationProfiles,
  assignPropsMat,
  propCI = FALSE,
  transType = "",
  yAxisLabel = ""
)

Arguments

protName	Name of the protein to plot
protProfile	protein profile
Nspectra	indicator for if there are columns in profile for Nspectra (number of spectra) and Npep (number of peptides)
pepProfile	peptide profiles
numRefCols	number of reference columns (preceding the data profile columns)
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, from the constrained proportional assignment algorithm, and optionally upper and lower 95 percent confidence limits
propCI	True if lower and upper confidence intervals are included in assignPros
transType	label for transformation; default is ""
yAxisLabel	label for y-axis

Value

plot of average, peptide, and reference profiles

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