mut_cna_volcano.Rnw

<<setup_mut_cna_volcano, include=FALSE>>=
library(dplyr)
library(magrittr)
df = import('data_frame')
plt = import('plot')
util = import('./util_2')
##TODO: %each>% || %>>% operator?
@

\begin{figure}[H]
<<mut_cna_volcao, echo=FALSE, fig.width=5, fig.height=8>>=
within = list(cna = filter(util$cna_cov, method == "speed_matrix"),
              mut = filter(util$mut_cov, method == "speed_matrix")) %>%
    df$bind_rows(name_col="type") %>%
    filter(adj.p < 0.05) %>%
    select(scores, m)

list(cna = filter(util$cna_cov, method == "speed_matrix"),
     mut = filter(util$mut_cov, method == "speed_matrix")) %>%
    df$bind_rows(name_col="type") %>%
    mutate(circle = df$contains(., within)) %>%
    plt$color$p_effect(pvalue="adj.p", effect="estimate", thresh=0.05, dir=-1) %>%
    mutate(color = ifelse(type=="cna" & adj.p < 0.05 & estimate > 0, "#44045745", color),
           color = ifelse(type=="cna" & adj.p < 0.05 & estimate < 0, "#c8e01e78", color)) %>%
    plt$volcano(base.size=0.1, text.size=2, p=0.05, label_top=Inf, ceil=1e-21)
@
\caption{Associatons for drivers/copy number alterations}
\label{fig:mut-heatmaps}
\end{figure}