protPepPlotfun: Plot reference compartment profiles overlaid with the profile...

In mooredf22/protlocassign: Estimation of protein distribution from quantitative subcellular fractionation experiments using a constrained proportional assignment model

Plot reference compartment profiles overlaid with the profile of a single protein and its component peptides

Description

This function creates a panel of plots, one for each compartment. Each plot contains a reference compartment profile overlaid with the profiles of one protein of interest and its component peptides as well as the CPA value for that compartment.

Usage

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

Arguments

protName	name of the protein to plot
protProfile	data frame containing protein profiles followed by columns named Npep and Nspectra for the numbers of peptides and spectra, respectively
pepProfile	data frame containing peptide profiles
numRefCols	number of reference columns in 'pepProfile' (preceding the data profile columns)
numDataCols	number of fractions in each profile
n.compartments	number of compartments
refLocationProfiles	data frame of profiles for the reference compartments
assignPropsMat	data frame containing CPA values
propCI	TRUE if lower and upper confidence intervals are included in assignPropsMat (not currently implemented)
transType	label for y-axis on each individual plot (default none))
yAxisLabel	label for y-axis of entire panel

Value

Plot of protein, peptide, and reference profiles

Examples

  # See Tutorial 6 for a full explanation

mooredf22/protlocassign documentation built on Sept. 13, 2023, 3:57 p.m.