## This code is part of the megaptera package
## © C. Heibl 2014 (last update 2014-12-19)
icContingency <- function(x, step = .05){
## PARAMETERS
## -----------
gene <- x@locus@sql
acc.tab <- paste("acc", gsub("^_", "", gene), sep = "_")
min.identity <- x@locus@min.identity
min.coverage <- x@locus@min.coverage
## open database connection
## ------------------------
conn <- dbconnect(x@db)
SQL <- paste("SELECT taxon,",
"max(identity) AS maxi, max(coverage) AS maxc",
"FROM", acc.tab,
"WHERE identity IS NOT NULL",
"AND coverage IS NOT NULL",
"AND status !~ 'excluded|too'",
"GROUP BY taxon")
z <- dbGetQuery(conn, SQL)
dbDisconnect(conn)
mi <- seq(0, 1, step)
mc <- seq(0, 1, step)
obj <- matrix(nrow = length(mi), ncol = length(mc),
dimnames = list(mi, mc))
for ( i in seq_along(mi)){
for ( j in seq_along(mc)){
obj[i, j] <- nrow(z[z$maxi >= mi[i] & z$maxc >= mc[j], ])
}
}
obj
}
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