This plots distribution of validation genes (4 by default) for validating the prediction result.
plotValidationGenes(es, PAM50.pred, genes = c("ESR1", "PGR", "MKI67", "ERBB2"))
| es | dataframe, rows are genes columns are samples. Row names has to be EntrezID. |
|---|---|
| PAM50.pred | array of each sample's PAM50 label |
| genes | (optional) vector of validation gene names |
Default 4 genes:
"ERBB2": Her2 gene; Her2 group should have the highest ERBB2 value.
"ESR1": ER gene; LumA and LumB groups should have the highest ESR1 value.
"MKI67": tumor growth factor; LumA should have the lowest MKI67 value because LumA patients usually have the best prognosis.
"PGR": PR gene; LumA should have the highest PGR value.