[R] Help with hclust() and plot()

[Sean Davis]

The use for par is:

> plot(1:8,1:8) #you must have an open graphics window before par has an effect
> par(mar=c(5,4,4,2)) #this will stay in effect until you either close the
graphics window or change it with another call to par
> plot(1:8,1:8)

In other words, par works on an open graphics device and applies to all
subsequent plots to that device.  You can't put it in the plot command--a
bit awkward at times, but often does save time and is very general.

Sean

On 5/21/04 7:51 AM, "michael watson (IAH-C)" <michael.watson at bbsrc.ac.uk>
wrote:

> Hi Sean
> 
> I obviously wasn't cut out for this.
> 
> Just to try it out, I tried:
> 
>> plot(1:8, 1:8, mar=c(5,4,4,2))
> 
> (this is the default according to the help)
> 
> All I got was:
> 
> "there were twelve warnings"
> 
>> warnings()
> 1: parameter "mar" couldn't be set in high-level plot() function
> 
> BUT in the help, the example is given as:
> 
> <highlevel plot> (..., <tag> = <value>)
> 
> So, I know I must be doing something stupid, but I have no idea what....
> 
> Mick
> 
> -----Original Message-----
> From: Sean Davis [mailto:sdavis2 at mail.nih.gov]
> Sent: 21 May 2004 12:30
> To: michael watson (IAH-C); sundar.dorai-raj at pdf.com
> Cc: r-help
> Subject: Re: [R] Help with hclust() and plot()
> 
> 
> See ?par.  It is a long help, but pay particular attention to
> par(mar=c(...)).  It changes margins on plots.
> 
> Sean
> 
> On 5/21/04 7:12 AM, "michael watson (IAH-C)"
> <michael.watson at bbsrc.ac.uk>
> wrote:
> 
>> OK, I have it working now
>> I just read in my data a little differently and now it works
>> 
>> HOWEVER, now my labels shoot off the end of the plot - so the labels
>> are truncated as they hit the edge of the window.  This happens for
>> both horizontal and vertical dendrograms
>> 
>> I guess this is an argument to plot that I need to set, but which one
>> ? :-(
>> 
>> Thanks
>> 
>> Mick
>> 
>> -----Original Message-----
>> From: michael watson (IAH-C)
>> Sent: 21 May 2004 11:53
>> To: sundar.dorai-raj at pdf.com
>> Cc: R-Help (E-mail)
>> Subject: RE: [R] Help with hclust() and plot()
>> 
>> 
>> Hi
>> 
>> Thanks again, but it *still* doesn't work!  I used the following
>> commands:
>> 
>>> eucomplete <- hclust(d = dist(p[, 2:13], method = "euclidean"),
>>> method
>> = "complete")
>>> eucomplete$labels
>> [1] "1"  "2"  "3"  "4"  "5"  "6"  "7"  "8"  "9"  "10" "11" "12" "13"
>> "14" "15" [16] "16" "17" "18" "19" "20" "21" "22" "23" "24"
>>> eucomplete$labels <- p[,1]
>>> eucomplete$labels
>> [1] NB Hippo S2_824   ME7 Hippo S2_0    ME7 Hippo S2_949  ME7 Hippo
>> S2_952
>> [5] ME7 Hippo S2_823  NB Hippo S2_819D  ME7 Hippo S2_772D ME7 Hippo
>> S2_#003
>> [9] NB Hippo S2_818D  NB Hippo S2_1     NB Hippo S2_#010  NB Hippo
>> S2_775D
>> [13] NB Hippo S2_774D  NB Hippo S2_#009  NB Hippo S2_950   NB Hippo
>> S2_826
>> [17] NB Hippo S2_#007  NB Hippo S2_951   ME7 Hippo S2_#004 ME7 Hippo
>> S2_820D
>> [21] ME7 Hippo S2_#005 ME7 Hippo S2_773D ME7 Hippo S2_#006 ME7 Hippo
>> S2_822D 24 Levels: ME7 Hippo S2_#003 ME7 Hippo S2_#004 ... NB Hippo
>> S2_951
>>> plot(as.dendrogram(eucomplete))
>> 
>> I get a lovely formatted dendrogram but the labels are still numbers
>> 1-24! :-(
>> 
>> As can be seen, I have changed eucomplete$labels to be the text I
>> want, but the plot command still writes out numbers :-(
>> 
>>> plot(eucomplete)
>> 
>> Does work, and I get the right labels.  But I want a dendrogram!
>> 
>> Thanks in advance for your help
>> 
>> Mick
>> 
>> 
>> 
>> -----Original Message-----
>> From: Sundar Dorai-Raj [mailto:sundar.dorai-raj at PDF.COM]
>> Sent: 20 May 2004 19:04
>> To: michael watson (IAH-C)
>> Cc: R-Help (E-mail)
>> Subject: Re: [R] Help with hclust() and plot()
>> 
>> 
>> 
>> 
>> michael watson (IAH-C) wrote:
>> 
>>> Hi
>>> 
>>> Thanks for that!  BUT if I use as.dendrogram, I can't use my labels
>>> anymore!
>>> 
>>> 
>>>> plot(hclust(...etc), labels=p[,1])
>>> 
>>> 
>>> Works fine.  But:
>>> 
>>> 
>>>> plot(as.dendrogram(hclust(...etc)), labels=p[,1])
>>> 
>>> 
>>> Gives me errors:
>>> 
>>> Error in axis(side, at, labels, tick, line, pos, outer, font, vfont,
>>> lty,  : location and label lengths differ, 6 != 24
>>> 
>>> I have 24 labels.  I have no idea where it gets 6 from!
>>> 
>>> My 'dendrogram' has '2 branches and 24 members total'.
>>> 
>>> SOOO, how do I get my dendrogram horizontal, or vertical for that
>>> matter, with useful labels instead of 1,2,3,4,5,etc
>>> 
>>> Thanks in advance for your help!
>>> 
>>> Mick
>>> 
>> 
>> Mick,
>>  Change the labels in hclust first:
>> 
>> data(USArrests)
>> hc <- hclust(dist(USArrests), "ave")
>> hc$labels <- 1:50
>> dend1 <- as.dendrogram(hc)
>> plot(dend1, horiz = TRUE)
>> 
>> --sundar
>> 
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