plotMultipleProtein: Visualization of multiple protein localizations

In TanerArslan/SubCellBarCode-R-Package: SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome

Description

Distributions of subcellular localizations of multiple proteins both ar the compartment and neighborhood level are plotted.

Usage

plotMultipleProtein(sampleClassification, proteinList)

Arguments

sampleClassification	data.frame; merged classification, combination of compartment and neighborhood classifications per protein.
proteinList	vector; protein gene symbol names.

Value

multipleProt.df

Examples

{

df <- loadData(SubCellBarCode::hcc827Ctrl)

c.prots <- calculateCoveredProtein(rownames(df), markerProteins[,1])

r.markers <- markerQualityControl(c.prots, df)

cls <- svmClassification(r.markers, df, markerProteins)

test.A <- cls[[1]]$svm.test.prob.out
test.B <- cls[[2]]$svm.test.prob.out

t.c.df <- computeThresholdCompartment(test.A, test.B)

t.n.df <- computeThresholdNeighborhood(test.A, test.B)

all.A <- cls[[1]]$all.prot.pred
all.B <- cls[[2]]$all.prot.pred

c.cls.df <- applyThresholdCompartment(all.A, all.B, t.c.df)

n.cls.df <- applyThresholdNeighborhood(all.A, all.B, t.n.df)

cls.df  <- mergeCls(c.cls.df, n.cls.df)

proteasome26s <- c("PSMA7", "PSMC3", "PSMB1", "PSMA1", "PSMA3","PSMA4",
"PSMA5", "PSMB4", "PSMB6", "PSMB5","PSMC2", "PSMC4", "PSMB3", "PSMB2",
"PSMD4", "PSMA6", "PSMC1", "PSMC5", "PSMC6", "PSMB7", "PSMD13")

multipleProt.df <- plotMultipleProtein(cls.df, "proteasome26s" )

}

TanerArslan/SubCellBarCode-R-Package documentation built on May 14, 2019, 9:38 a.m.