protPlotfun: 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

Description

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

Usage

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

Arguments

protName	name of the protein to plot
profile	data frame of specified protein(row name) profiles
numDataCols	number of fractions in each profile
n.compartments	number of compartments (8 in Jadot data)
refLocationProfiles	data frame of profiles for the reference compartments
assignPropsMat	data frame containing CPA estimates
transType	label for y-axis on each individual plot (default none))
yAxisLabel	label for y-axis of entire panel

Value

A panel of profile plots

Examples

data(protNSA_test)
data(markerListJadot)
data(refLocProfNSA)
protCPAfromNSA_out <- fitCPA(profile=protNSA_test,
                              refLocationProfiles=refLocProfNSA,
                              numDataCols=9)
# Note that the profile of one protein, AIF1, contains missing values
# which causes the cpa routine to generate a nonconvergence message 

protPlotfun(protName="TLN1", profile=protNSA_test,
            numDataCols=9, n.compartments=8,
            refLocationProfiles=refLocProfNSA,
            assignPropsMat=protCPAfromNSA_out,
            yAxisLabel="Normalized Specific Amount")

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