Aleš Žiberna wrote:
Hello!
I have the following problem.
I would like to plot the hclust object "hcd" (bellow, at the end of the
mail) with ticks at seq(0.05,0.25,by=0.05). I tried using the code
plot(hcd)
and
plot(hcd,axes=FALSE)
axis(2,seq(0.05,0.25,by=0.05))
In both cases, the resoult is the same, ticks at 0.05 and 0.25 are not
printed. I tried changing the ylim argumet in plot, however I got a
warning "parameter "ylim" couldn't be set in high-level plot() function".
I would like to force those two ticks. Can this be done with axis or
plot, or should I use "lines"?
Not easy with the plot method for a hclust object, because 0.05 and 0.25
are getting clipped, because they are out od the "usr" coordinated of
the plot.
Of course you could hack plot.hclust (in Namespace stats) by modifying
.../R/library/src/stats/R/hclust.R as follows (in order to provide a
proper ylim argument):
diff hclust.R-orig hclust.R
91c91,92
< sub = NULL, xlab = NULL, ylab = "Height", ...)
---
> sub = NULL, xlab = NULL, ylab = "Height",
> ylim = NULL, ...)
116c117,120
< .Internal(dend.window(n, merge, height, hang, labels, ...))
---
> height2 <- height
> if(!is.null(ylim))
> height2 <- c(range(ylim), rep(ylim[1], length(height) - 2))
> .Internal(dend.window(n, merge, height2, hang, labels, ...))
Note that this quick hack is a *dirty* solution.
Uwe Ligges
Thanks in advance for any suggestions!
Aleš Žiberna
"hcd" <-
structure(list(merge = structure(as.integer(c(-4, -5, -1, -7,
-6, -10, -3, -12, -8, -2, 8, 1, -9, -11, 2, 3, -13, 4, 6, 5,
7, 9, 10, 11)), .Dim = as.integer(c(12, 2))), height =
c(0.0906288626438465,
0.10278145998519, 0.114885217561497, 0.127812745765521, 0.132377986666522,
0.168594637784091, 0.177187802444346, 0.209803430657638, 0.210361529934791,
0.218946973173863, 0.234000873708654, 0.235702383243089), order =
as.integer(c(4,
9, 12, 6, 13, 2, 8, 3, 10, 7, 1, 5, 11)), labels = NULL, method = "single",
call = quote(hclust(d = d, method = "single")), dist.method = NULL),
.Names = c("merge",
"height", "order", "labels", "method", "call", "dist.method"), class =
"hclust")
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