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

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From: Sean Davis (sdavis2@mail.nih.gov)
Date: Fri 21 May 2004 - 21:56:02 EST


Message-id: <BCD36692.8369%sdavis2@mail.nih.gov>

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@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@mail.nih.gov]
> Sent: 21 May 2004 12:30
> To: michael watson (IAH-C); sundar.dorai-raj@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@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@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@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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>> PLEASE do read the posting guide!
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>>
>> ______________________________________________
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>>
>

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