Re: [R] Forcing ticks in plot for hclust object outside the limits
Thank you very much for your reply and your *dirty* sloution, which does the trick for me! Ale iberna - Original Message - From: Uwe Ligges [EMAIL PROTECTED] To: Ale iberna [EMAIL PROTECTED] Cc: R-help r-help@stat.math.ethz.ch Sent: Saturday, May 28, 2005 7:58 PM Subject: Re: [R] Forcing ticks in plot for hclust object outside the limits Ale iberna 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! Ale iberna 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, 0.13237798522, 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) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Forcing ticks in plot for hclust object outside the limits
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? Thanks in advance for any suggestions! Ale iberna 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, 0.13237798522, 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) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Forcing ticks in plot for hclust object outside the limits
Ale iberna 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! Ale iberna 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, 0.13237798522, 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) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
