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Wittner, Ben

2005-Aug-22 21:48 UTC

[R] problem building dendrograms to use with heatmap()

Hi,

I'm trying to build dendrograms to pass to heatmap().
The dendrograms I build plot properly, but when I pass them to heatmap() I get
the error message "row dendrogram ordering gave index of wrong length"
(see
output log below).
I looked in the code of heatmap() and saw that the error was due to a NULL
return value from order.dendrogram(), which in turn got a NULL return value from
unlist(). But I have no idea why unlist() is returning NULL.

I've included code below which reproduces the problem and below that the
output
from a run of that code on my computer.

Any help would be greatly appreciated. Thanks in advance.

-Ben

###########################  begin code  ###################################

version

dendro.leaf <- function(label) {
  ans <- list()
  attr(ans, 'members') <- 1
  attr(ans, 'height') <- 0
  attr(ans, 'leaf') <- T
  attr(ans, 'midpoint') <- 0
  attr(ans, 'label') <- label
  attr(ans, 'class') <- 'dendrogram'
  ans
}

dendro.merge <- function(d1, d2, height) {
  ans <- list(d1, d2)
  members <- attr(d1, 'members') + attr(d2, 'members')
  attr(ans, 'members') <- members
  attr(ans, 'height') <- height
  attr(ans, 'leaf') <- F
  attr(ans, 'midpoint') <- (members - 1)/2
  attr(ans, 'class') <- 'dendrogram'
  ans
}

lc1 <- dendro.leaf('c1')
lc2 <- dendro.leaf('c2')
lc3 <- dendro.leaf('c3')
nc1 <- dendro.merge(lc1, lc2, 0.1)
nc2 <- dendro.merge(nc1, lc3, 0.2)
plot(nc2)

lr1 <- dendro.leaf('r1')
lr2 <- dendro.leaf('r2')
lr3 <- dendro.leaf('r3')
nr1 <- dendro.merge(lr2, lr3, 0.1)
nr2 <- dendro.merge(lr1, nr1, 0.3)
plot(nr2)

x <- matrix(seq(-1, 1, length.out=9), nrow=3)
rownames(x) <- paste('r', 1:3, sep='')
colnames(x) <- paste('c', 1:3, sep='')

heatmap(x, Rowv=nr2, Colv=nc2, scale='none')

order.dendrogram(nr2)

unlist(nr2)

###############  begin output from run of code above  ##################
> version         _                
platform i686-pc-linux-gnu
arch     i686             
os       linux-gnu        
system   i686, linux-gnu  
status                    
major    2                
minor    1.1              
year     2005             
month    06               
day      20               
language R                > 
> dendro.leaf <- function(label) {+   ans <- list()
+   attr(ans, 'members') <- 1
+   attr(ans, 'height') <- 0
+   attr(ans, 'leaf') <- T
+   attr(ans, 'midpoint') <- 0
+   attr(ans, 'label') <- label
+   attr(ans, 'class') <- 'dendrogram'
+   ans
+ }> 
> dendro.merge <- function(d1, d2, height) {+   ans <- list(d1, d2)
+   members <- attr(d1, 'members') + attr(d2, 'members')
+   attr(ans, 'members') <- members
+   attr(ans, 'height') <- height
+   attr(ans, 'leaf') <- F
+   attr(ans, 'midpoint') <- (members - 1)/2
+   attr(ans, 'class') <- 'dendrogram'
+   ans
+ }> 
> lc1 <- dendro.leaf('c1')
> lc2 <- dendro.leaf('c2')
> lc3 <- dendro.leaf('c3')
> nc1 <- dendro.merge(lc1, lc2, 0.1)
> nc2 <- dendro.merge(nc1, lc3, 0.2)
> plot(nc2)
> 
> lr1 <- dendro.leaf('r1')
> lr2 <- dendro.leaf('r2')
> lr3 <- dendro.leaf('r3')
> nr1 <- dendro.merge(lr2, lr3, 0.1)
> nr2 <- dendro.merge(lr1, nr1, 0.3)
> plot(nr2)
> 
> x <- matrix(seq(-1, 1, length.out=9), nrow=3)
> rownames(x) <- paste('r', 1:3, sep='')
> colnames(x) <- paste('c', 1:3, sep='')
> 
> heatmap(x, Rowv=nr2, Colv=nc2, scale='none')Error in heatmap(x, Rowv = nr2, Colv = nc2, scale = "none") : 
        row dendrogram ordering gave index of wrong
length> 
> order.dendrogram(nr2)
NULL> 
> unlist(nr2)
NULL>

Paul Murrell

2005-Aug-25 23:37 UTC

head link

[R] problem building dendrograms to use with heatmap()

Hi


Wittner, Ben wrote:> Hi,
> 
> I'm trying to build dendrograms to pass to heatmap().
> The dendrograms I build plot properly, but when I pass them to heatmap() I
get
> the error message "row dendrogram ordering gave index of wrong
length" (see
> output log below).

Looks like you're not building the dendrograms "properly". 
Compare
unclass(nr2) with unclass() of a dendrogram from 
as.dendrogram(hclust(<something>)).  You might need to look closely at 
stats:::as.dendrogram.hclust to get it right.

Paul

> I looked in the code of heatmap() and saw that the error was due to a NULL
> return value from order.dendrogram(), which in turn got a NULL return value
from
> unlist(). But I have no idea why unlist() is returning NULL.
> 
> I've included code below which reproduces the problem and below that
the output
> from a run of that code on my computer.
> 
> Any help would be greatly appreciated. Thanks in advance.
> 
> -Ben
> 
> ###########################  begin code 
###################################
> 
> version
> 
> dendro.leaf <- function(label) {
>   ans <- list()
>   attr(ans, 'members') <- 1
>   attr(ans, 'height') <- 0
>   attr(ans, 'leaf') <- T
>   attr(ans, 'midpoint') <- 0
>   attr(ans, 'label') <- label
>   attr(ans, 'class') <- 'dendrogram'
>   ans
> }
> 
> dendro.merge <- function(d1, d2, height) {
>   ans <- list(d1, d2)
>   members <- attr(d1, 'members') + attr(d2, 'members')
>   attr(ans, 'members') <- members
>   attr(ans, 'height') <- height
>   attr(ans, 'leaf') <- F
>   attr(ans, 'midpoint') <- (members - 1)/2
>   attr(ans, 'class') <- 'dendrogram'
>   ans
> }
> 
> lc1 <- dendro.leaf('c1')
> lc2 <- dendro.leaf('c2')
> lc3 <- dendro.leaf('c3')
> nc1 <- dendro.merge(lc1, lc2, 0.1)
> nc2 <- dendro.merge(nc1, lc3, 0.2)
> plot(nc2)
> 
> lr1 <- dendro.leaf('r1')
> lr2 <- dendro.leaf('r2')
> lr3 <- dendro.leaf('r3')
> nr1 <- dendro.merge(lr2, lr3, 0.1)
> nr2 <- dendro.merge(lr1, nr1, 0.3)
> plot(nr2)
> 
> x <- matrix(seq(-1, 1, length.out=9), nrow=3)
> rownames(x) <- paste('r', 1:3, sep='')
> colnames(x) <- paste('c', 1:3, sep='')
> 
> heatmap(x, Rowv=nr2, Colv=nc2, scale='none')
> 
> order.dendrogram(nr2)
> 
> unlist(nr2)
> 
> ###############  begin output from run of code above  ##################
> 
> 
>>version
> 
>          _                
> platform i686-pc-linux-gnu
> arch     i686             
> os       linux-gnu        
> system   i686, linux-gnu  
> status                    
> major    2                
> minor    1.1              
> year     2005             
> month    06               
> day      20               
> language R                
> 
>>dendro.leaf <- function(label) {
> 
> +   ans <- list()
> +   attr(ans, 'members') <- 1
> +   attr(ans, 'height') <- 0
> +   attr(ans, 'leaf') <- T
> +   attr(ans, 'midpoint') <- 0
> +   attr(ans, 'label') <- label
> +   attr(ans, 'class') <- 'dendrogram'
> +   ans
> + }
> 
>>dendro.merge <- function(d1, d2, height) {
> 
> +   ans <- list(d1, d2)
> +   members <- attr(d1, 'members') + attr(d2, 'members')
> +   attr(ans, 'members') <- members
> +   attr(ans, 'height') <- height
> +   attr(ans, 'leaf') <- F
> +   attr(ans, 'midpoint') <- (members - 1)/2
> +   attr(ans, 'class') <- 'dendrogram'
> +   ans
> + }
> 
>>lc1 <- dendro.leaf('c1')
>>lc2 <- dendro.leaf('c2')
>>lc3 <- dendro.leaf('c3')
>>nc1 <- dendro.merge(lc1, lc2, 0.1)
>>nc2 <- dendro.merge(nc1, lc3, 0.2)
>>plot(nc2)
>>
>>lr1 <- dendro.leaf('r1')
>>lr2 <- dendro.leaf('r2')
>>lr3 <- dendro.leaf('r3')
>>nr1 <- dendro.merge(lr2, lr3, 0.1)
>>nr2 <- dendro.merge(lr1, nr1, 0.3)
>>plot(nr2)
>>
>>x <- matrix(seq(-1, 1, length.out=9), nrow=3)
>>rownames(x) <- paste('r', 1:3, sep='')
>>colnames(x) <- paste('c', 1:3, sep='')
>>
>>heatmap(x, Rowv=nr2, Colv=nc2, scale='none')
> 
> Error in heatmap(x, Rowv = nr2, Colv = nc2, scale = "none") : 
>         row dendrogram ordering gave index of wrong length
> 
>>order.dendrogram(nr2)
> 
> NULL
> 
>>unlist(nr2)
> 
> NULL
> 
> 
> ______________________________________________
> R-help at 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

-- 
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
paul at stat.auckland.ac.nz
http://www.stat.auckland.ac.nz/~paul/

Wittner, Ben

2005-Aug-29 13:37 UTC

head link

[R] problem building dendrograms to use with heatmap()

Thanks Paul.

It seems there's an undocumented requirement that in order to use a
dendrogram
as an argument to heatmap(),
(a) the leaf nodes must be integers indicating the leaf's position in the
left-to-right ordering of the leafs and/or
(b) only the root of the dendrogram can be of class dendrogram.

I discovered this by doing as you suggested below and with some help from Jeff
Gentry.

-Ben
> -----Original Message-----
> From: Paul Murrell [mailto:p.murrell at auckland.ac.nz]
> Sent: Thursday, August 25, 2005 7:37 PM
> To: Wittner, Ben
> Cc: r-help at stat.math.ethz.ch
> Subject: Re: [R] problem building dendrograms to use with heatmap()
> 
> Hi
> 
> 
> Wittner, Ben wrote:
> > Hi,
> >
> > I'm trying to build dendrograms to pass to heatmap().
> > The dendrograms I build plot properly, but when I pass them to
heatmap()
> I get
> > the error message "row dendrogram ordering gave index of wrong
length"
> (see
> > output log below).
> 
> 
> Looks like you're not building the dendrograms "properly". 
Compare
> unclass(nr2) with unclass() of a dendrogram from
> as.dendrogram(hclust(<something>)).  You might need to look closely
at
> stats:::as.dendrogram.hclust to get it right.
> 
> Paul
> 
> 
> > I looked in the code of heatmap() and saw that the error was due to a
> NULL
> > return value from order.dendrogram(), which in turn got a NULL return
> value from
> > unlist(). But I have no idea why unlist() is returning NULL.
> >
> > I've included code below which reproduces the problem and below
that the
> output
> > from a run of that code on my computer.
> >
> > Any help would be greatly appreciated. Thanks in advance.
> >
> > -Ben
> >
> > ###########################  begin code
> ###################################
> >
> > version
> >
> > dendro.leaf <- function(label) {
> >   ans <- list()
> >   attr(ans, 'members') <- 1
> >   attr(ans, 'height') <- 0
> >   attr(ans, 'leaf') <- T
> >   attr(ans, 'midpoint') <- 0
> >   attr(ans, 'label') <- label
> >   attr(ans, 'class') <- 'dendrogram'
> >   ans
> > }
> >
> > dendro.merge <- function(d1, d2, height) {
> >   ans <- list(d1, d2)
> >   members <- attr(d1, 'members') + attr(d2,
'members')
> >   attr(ans, 'members') <- members
> >   attr(ans, 'height') <- height
> >   attr(ans, 'leaf') <- F
> >   attr(ans, 'midpoint') <- (members - 1)/2
> >   attr(ans, 'class') <- 'dendrogram'
> >   ans
> > }
> >
> > lc1 <- dendro.leaf('c1')
> > lc2 <- dendro.leaf('c2')
> > lc3 <- dendro.leaf('c3')
> > nc1 <- dendro.merge(lc1, lc2, 0.1)
> > nc2 <- dendro.merge(nc1, lc3, 0.2)
> > plot(nc2)
> >
> > lr1 <- dendro.leaf('r1')
> > lr2 <- dendro.leaf('r2')
> > lr3 <- dendro.leaf('r3')
> > nr1 <- dendro.merge(lr2, lr3, 0.1)
> > nr2 <- dendro.merge(lr1, nr1, 0.3)
> > plot(nr2)
> >
> > x <- matrix(seq(-1, 1, length.out=9), nrow=3)
> > rownames(x) <- paste('r', 1:3, sep='')
> > colnames(x) <- paste('c', 1:3, sep='')
> >
> > heatmap(x, Rowv=nr2, Colv=nc2, scale='none')
> >
> > order.dendrogram(nr2)
> >
> > unlist(nr2)
> >
> > ###############  begin output from run of code above 
##################
> >
> >
> >>version
> >
> >          _
> > platform i686-pc-linux-gnu
> > arch     i686
> > os       linux-gnu
> > system   i686, linux-gnu
> > status
> > major    2
> > minor    1.1
> > year     2005
> > month    06
> > day      20
> > language R
> >
> >>dendro.leaf <- function(label) {
> >
> > +   ans <- list()
> > +   attr(ans, 'members') <- 1
> > +   attr(ans, 'height') <- 0
> > +   attr(ans, 'leaf') <- T
> > +   attr(ans, 'midpoint') <- 0
> > +   attr(ans, 'label') <- label
> > +   attr(ans, 'class') <- 'dendrogram'
> > +   ans
> > + }
> >
> >>dendro.merge <- function(d1, d2, height) {
> >
> > +   ans <- list(d1, d2)
> > +   members <- attr(d1, 'members') + attr(d2,
'members')
> > +   attr(ans, 'members') <- members
> > +   attr(ans, 'height') <- height
> > +   attr(ans, 'leaf') <- F
> > +   attr(ans, 'midpoint') <- (members - 1)/2
> > +   attr(ans, 'class') <- 'dendrogram'
> > +   ans
> > + }
> >
> >>lc1 <- dendro.leaf('c1')
> >>lc2 <- dendro.leaf('c2')
> >>lc3 <- dendro.leaf('c3')
> >>nc1 <- dendro.merge(lc1, lc2, 0.1)
> >>nc2 <- dendro.merge(nc1, lc3, 0.2)
> >>plot(nc2)
> >>
> >>lr1 <- dendro.leaf('r1')
> >>lr2 <- dendro.leaf('r2')
> >>lr3 <- dendro.leaf('r3')
> >>nr1 <- dendro.merge(lr2, lr3, 0.1)
> >>nr2 <- dendro.merge(lr1, nr1, 0.3)
> >>plot(nr2)
> >>
> >>x <- matrix(seq(-1, 1, length.out=9), nrow=3)
> >>rownames(x) <- paste('r', 1:3, sep='')
> >>colnames(x) <- paste('c', 1:3, sep='')
> >>
> >>heatmap(x, Rowv=nr2, Colv=nc2, scale='none')
> >
> > Error in heatmap(x, Rowv = nr2, Colv = nc2, scale = "none")
:
> >         row dendrogram ordering gave index of wrong length
> >
> >>order.dendrogram(nr2)
> >
> > NULL
> >
> >>unlist(nr2)
> >
> > NULL
> >
> >
> > ______________________________________________
> > R-help at 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
> 
> 
> --
> Dr Paul Murrell
> Department of Statistics
> The University of Auckland
> Private Bag 92019
> Auckland
> New Zealand
> 64 9 3737599 x85392
> paul at stat.auckland.ac.nz
> http://www.stat.auckland.ac.nz/~paul/

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