| 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)
}