mixturePlot: Plot sets of simulated proteins distributed between two...

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

Plot sets of simulated proteins distributed between two compartments.

Description

For a set of simulated proteins distributed between two compartments, plot the CPA estimates from a given type of profile versus true mixture proportions.

Usage

mixturePlot(
  mixProtiProtjCPA,
  NstartMaterialFractions = 6,
  Loc1,
  Loc2,
  increment.prop = 0.1,
  errorReturn = FALSE,
  subTitle = NULL,
  xaxisLab = TRUE,
  yaxisLab = TRUE
)

Arguments

mixProtiProtjCPA	data frame of CPA estimates for each set of two compartment mixtures
NstartMaterialFractions	Number of fractions that reconstitute the starting material, e.g., a complete set of differential centrifugation fractions. For experiment AT5, it is 6 ( N, M, L1, L2, P, and S).
Loc1	row number of subcellular location 1 of mixture
Loc2	row number of subcellular location 2 of mixture
increment.prop	increments in proportion residing in Loc1 (from 0 to 1); Default is 0.1
errorReturn	return area of error region if TRUE
subTitle	subtitle for plot if present; NULL if not (default)
xaxisLab	plot label for x-axis if TRUE
yaxisLab	plot label for y-axis if TRUE

Value

Plot CPA estimates versus true mixture proportions.

Examples

data(protNSA_test)
data(markerListJadot)
data(totProtAT5)
data(refLocProfAcup)
data(refLocProfNSA)

mixCytoLysoAcup <- proteinMix(AcupRef= refLocProfAcup,
                              increment.prop=0.1,
                              Loc1=1, Loc2=4)
# Convert mixture Acup profiles to NSA profiles
mixCytoLysoNSA <- NSAfromAcup(Acup=mixCytoLysoAcup,
                      NstartMaterialFractions=6, totProt=totProtAT5)
                      
# Find constrained proportional values
mixCytoLysoCPAfromNSA <- fitCPA(profile=mixCytoLysoNSA,
                                refLocationProfiles=refLocProfNSA,
                                numDataCols=9)

# Plot the mixtures and fitted values and print the error
library(pracma)
mixturePlot(mixProtiProtjCPA=mixCytoLysoCPAfromNSA,
            NstartMaterialFractions=6, Loc1=1, Loc2=4,
            increment.prop=0.1, xaxisLab=TRUE, yaxisLab=TRUE,
            errorReturn = TRUE)
            

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