cna_mut_compare.Rnw

<<setup_cna_mut_compare, include=FALSE>>=
library(magrittr)
util = import('./util_2')

cov_keep = bind_rows(util$mut_cov, util$cna_cov) %>%
    group_by(m) %>%
    filter(any(-log10(adj.p) > 5)) %>%
    top_n(1, -adj.p) %>%
    ungroup() %>%
    select(m, adj.p) %>%
    arrange(adj.p) %$%
    setNames(adj.p, m)
@

\begin{figure}[H]
\subfloat[RTK/MAPK related]{
<<method_compare1, echo=FALSE, fig.width=15, fig.height=5>>=
util$mut_grid("KRAS_amp", "ERBB2_amp", "MYC_amp", "FGFR1_amp", nrow=1)
@
}

\subfloat[Cell-cycle related]{
<<method_compare2, echo=FALSE, fig.width=15, fig.height=5>>=
util$mut_grid("CDK12_amp", "CDKN2A_del", "CDKN1B_amp", "EIF4A2_amp", nrow=1)
@
}

\subfloat[PI3K signaling]{
<<method_compare3, echo=FALSE, fig.width=15, fig.height=5>>=
util$mut_grid("PTEN_del", "PIK3CA_amp", "PIK3CB_amp", "PIK3C2B_amp", nrow=1)
@
}

\subfloat[Uncategorized]{
<<method_compare4, echo=FALSE, fig.width=15, fig.height=5>>=
util$mut_grid("CTNNB1", "NOTCH2_amp", "GATA3_amp", "CASP8_amp", nrow=1)
@
}

\caption{Comparison of mutation associations across methods}
\label{fig:drug-compare-matrix}
\end{figure}