plotBarcode: Visualize the SubCellBarCode

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

Description

Stacked bar plot are plotted for compartment and neighborhood level with respect to classification probabilities.

Usage

plotBarcode(sampleClassification, protein, s1PSM)

Arguments

sampleClassification	data.frame; merged classification, combination of compartment and neighborhood classification.
protein	character; protein gene symbol name
s1PSM	data.frame; minimum PSM count table. Row names should be gene centric protein id.

Value

proteinPlot

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)

proteinPlot <- plotBarcode(cls.df, "TP53", hcc827CtrlPSMCount)
}

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