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Closes #3 #4

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Closes #3 #4

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16 changes: 9 additions & 7 deletions R/plot.Intervals_virtual.R
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Original file line number Diff line number Diff line change
Expand Up @@ -8,19 +8,20 @@ plot.Intervals_full <- function(
use_points = TRUE,
use_names = TRUE,
names_cex = 1,
text_col = NULL,
...
)
{
# Subset first, for efficiency, and so that the maximal y plotted is
# appropriate for the region shown.

if ( any( is.na( x ) ) ) x <- x[ !is.na(x), ]

if ( is.null(xlim) )
xlim <- range( x@.Data )
else
x <- x[ x[,2] >= xlim[1] & x[,1] <= xlim[2], ]

if ( is.null(y) )
y <- .Call( "_plot_overlap", x@.Data, closed(x), is( x, "Intervals_full" ) )

Expand All @@ -42,14 +43,14 @@ plot.Intervals_full <- function(
col = col,
lwd = lwd
)
if ( use_points ) {
if ( use_points ) {
# Careful with points...
adjust <- ( x[,1] == x[,2] ) & !closed(x)[,1]
closed(x)[ adjust, 2 ] <- FALSE
points(
x@.Data, rep( y, 2 ),
pch = 21, cex = cex,
col = col, bg = ifelse( closed(x), col, "white" )
col = col, bg = ifelse( closed(x), col, "white" )
)
}
if ( use_names && !is.null( rownames(x) ) ) {
Expand All @@ -59,12 +60,13 @@ plot.Intervals_full <- function(
rownames( x ),
pos = 3, offset = .5,
cex = names_cex,
xpd = NA
)
xpd = NA,
col = text_col
)
}
if ( axes )
axis( 1 )
}
}

plot.Intervals <- function( x, y = NULL, ... ) {
plot( as( x, "Intervals_full" ), y, ... )
Expand Down
7 changes: 6 additions & 1 deletion man/plot.Intervals.Rd
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@
use_points = TRUE,
use_names = TRUE,
names_cex = 1,
text_col = NULL,
...
)

Expand Down Expand Up @@ -84,6 +85,10 @@
TRUE}.
}

\item{text_col}{
Color of printed labels. Only relevant if \code{use_names = TRUE}.
}

\item{...}{Other arguments for \code{\link{plot.default}}.}

}
Expand Down Expand Up @@ -149,4 +154,4 @@ x <- Intervals( cbind( left, right ) )

plot(x, use_points=FALSE)
plot(x, use_points=FALSE, xlim = c(0, 500))
}
}