plotBarcode {SubCellBarCode} | R Documentation |
Stacked bar plot are plotted for compartment and neighborhood level with respect to classification probabilities.
plotBarcode(sampleClassification, protein, s1PSM)
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. |
proteinPlot
{ #create mock data plot.df <- data.frame(Protein = "TP53", NeighborhoodCls = "Nuclear", CompartmentCls = "N1", Secretory = as.numeric(0.01), Nuclear = as.numeric(0.95), Cytosol = as.numeric(0.02), Mitochondria = as.numeric(0.02), S1 = as.numeric(0.02), S2 = as.numeric(0.02), S3 = as.numeric(0.02), S4 = as.numeric(0.02), N1 = as.numeric(0.72), N2 = as.numeric(0.02), N3 = as.numeric(0.02), N4 = as.numeric(0.02), C1 = as.numeric(0.02), C2 = as.numeric(0.02), C3 = as.numeric(0.02), C4 = as.numeric(0.02), C5 = as.numeric(0.02), M1 = as.numeric(0.02), M2 = as.numeric(0.02)) rownames(plot.df) <- "TP53" psm.df <- data.frame(Protein = "TP53", PSMs.for.quant = as.numeric(31)) rownames(psm.df) <- "TP53" proteinPlot <- plotBarcode(plot.df, "TP53", psm.df) }