protPepPlotfun: Plot profiles of reference proteins

In mooredf22/protsummarize2:

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,
  protProfileSummary,
  Nspectra = T,
  finalList = NULL,
  protPepData = NULL,
  refCol = 5,
  n.fractions = 9,
  n.compartments = 8,
  markerLocR = markerLocRuse,
  assignPropsMat = assignPropsUse,
  propCI = F,
  transType = "",
  yAxisLabel = ""
)

Arguments

protName	Name of the protein to plot
protProfileSummary	data frame of protein names and their relative abundance levels..
Nspectra	indicator for if there are columns in protProfileSummary for Nspectra (number of spectra) and Npep (number of peptides)
finalList	spectrum-level abundance levels by protein and peptide; Ehis is NULL if not available
n.fractions	number of fractions per protein
n.compartments	number of compartments (8 in Jadot data)
markerLocR	A matrix markerLocR giving the abundance level profiles of the subcellular locations n.compartments = 8 columns are subcellular locations, and n.fractions 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
refLocProteins	List of reference proteins
predictedProp.mat	A matrix of CPA predicted proportions, from proLocAll
confint	indicator for if there are standard errors (from bootstrapping) for the assigned proportions (in protProfileSummary)
predictedPropL.mat	Matrix of lower confidence limits, one row for each protein, and 9 columns of lower confidence interval limits
predictedPropU.mat	Matrix of upper confidence limits, one row for each protein, and 9 columns of upper confidence interval limits

mooredf22/protsummarize2 documentation built on May 16, 2021, 10:12 p.m.