mutation analysis, top mutations, maftools

Question

[Rob]

Hi friends, I am using maftools to analyze for mutation. this is my code for cooncoplot :

coOncoplot(m1 = maf1, m2 = maf2, m1Name = 'Tumor',
m2Name = 'Control', genes = c("VHL", "PBRM1", "TTN",
"BAP1", "KDM5C", "ATM","MTOR", "ABTB2","FBN2", "SETD2", "BRINP2"),
removeNonMutated = FALSE)

this is my plot:

enter link description here

when I set removeNonMutated = FALSE and removeNonMutated = TRUE the resulted plots are the same. anyone can tell me why number of sample stays the same in both? I try to solve my power problem by setting removeNonMutated = FALSE but I could not make it work.