[BioC] heatplot() 1. red-*black*-green palette, 2.suppress drawing of the row dendrogram (but NOT row reordering)

[Heidi Dvinge]

> Hi Heidi,
>
> Thank you for your thoughts and suggestions,
>
> On 8/7/2010 6:49 PM, Heidi Dvinge wrote:
>> Hello Karl,
>>
>> I'm not familiar with the made4 package, but it looks like some of the
>> changes you want cannot override the defaults from heatplot. Are there
>> any
>> particular reason why you don't want to use heatmap.2 directly? Using
>> your
>> example from below, then
>
> The stated defaults of heatplot() follow the methodology by Eisen et al
> 1998. This is my starting point, and i must admit, my data 'looks' v.
> good using these distance (Pearson Correlation coefficient) and linkage
> (average) methods.
>
Is something like this more what you're after?

library(gplots)
my.mat<- matrix(rnorm(250), nrow=50, ncol=5)
dist.pear <- function(x) as.dist(1-cor(t(x)))
hclust.ave <- function(x) hclust(x, method="average")

heatmap.2(my.mat, col=c(redgreen(256)), dendrogram="col", trace="none",
density.info="none", distfun=dist.pear, hclustfun=hclust.ave)

Although, looking at the heatplot function they use a slightly different 
function to calculate the distance.

distEisen <- function(x, use = "pairwise.complete.obs") {
        co.x <- cor(x, use = use)
        dist.co.x <- 1 - co.x
        return(as.dist(dist.co.x))
}

HTH
\Heidi

> *If* i knew how to implement these in heatmap.2() i would. I assume the
> arguments: "hclustfun =" and "distfun =" could be modified to deliver
> what ever i want, including Pearson Correlation coefficient and linkage
> average linkage methods. But it would be trial, error and googling to
> acheive this. Which is my next step, unless some one has the patience to
> provide an example or point me to one (cheers!). So this is my sole
> reason for using heatplot over heatmap.2 (or heatmap).
>
>>
>> library(gplots)
>> my.mat<- matrix(rnorm(250), nrow=50, ncol=5)
>> heatmap.2(my.mat, col=c(redgreen(256)), dendrogram="col", trace="none",
>> density.info="none")
>>
>> will give you something similar to
>>
>> heatplot(my.mat, dend="both", cols.default=TRUE)
>>
>> only with the colours you want, and without the row dendrogram (but with
>> row reordering).
>>
>> If you want to use heatplot() because you actually have some made4
>> defined
>> object and not a matrix to begin with, then note that the first couple
>> of
>> lines in the heatplot() code are
>>
>> data<- array2ade4(dataset)
>> data<- as.matrix(data)
>>
>> Presumably you can call something like that on your data first, to get a
>> matrix that can be plotted with heatmap.2
>>
>> On an different note, then green-black-red isn't really the optimal
>> colour
>> scheme due to the number of red/green colour blind people. Consider
>> using
>> maybe blue-black-yellow or something else instead.
>
> I never considered this aspect. Indeed i will.
>
> Thanks again for your thoughts and any further ones you (or anyone else)
> may have,
>
> Karl
>
> The RColorBrewer
>> package also has a range of pre-defined colour schemes. Check out e.g.
>> display.brewer.all(9)
>>
>> HTH
>> \Heidi
>>
>>> Hi Jim,
>>>
>>> Sorry- guilty of impatience/laziness.
>>>
>>> Find below what i ran on my machine and the errors i received. I
>>> thought
>>> given heatplot() is based on heatmap.2(), i could just use some
>>> heatmap.2() arguments to get what i wanted. I failed and lack the
>>> understanding to modify heatplot() myself to achieve my goal-
>>> red-BLACK-green colors and suppressing drawing of the row dendrogram.
>>>
>>> All tips greatly appreciated,
>>>
>>> Karl
>>>
>>> ###run local###
>>> # Bioc examples heatplot() returned errors:
>>> library(made4)
>>> my.mat<- matrix(rnorm(250), nrow=50, ncol=5)
>>>
>>> # 1. default works fine:
>>> windows()
>>> plot.new()
>>> heatplot(my.mat, dend="both", cols.default=TRUE)
>>>
>>> # 2. attempt  red/black/green palette with hetamap.2 col= arg
>>> windows()
>>> plot.new()
>>> heatplot(my.mat, dend="both", cols.default=FALSE, col =
>>> c(redgreen(256)))
>>>
>>> # 3. attempt to supress drawing row dendrogram tree not NOT row
>>> reordering
>>> windows()
>>> plot.new()
>>> heatplot(my.mat, dend="both", cols.default=TRUE, dendrogram = "column")
>>>
>>> ###end
>>>
>>> #2. returned:
>>>   >Error in heatmap.2(data, Colv = Colv, Rowv = Rowv, col = plotcols,
>>> scale = scale,  :
>>>   >   formal argument "col" matched by multiple actual arguments
>>>
>>> #3. returned:
>>>   >Error in heatmap.2(data, Colv = Colv, Rowv = Rowv, col = plotcols,
>>> scale = scale,  :
>>>   >   formal argument "dendrogram" matched by multiple actual arguments
>>>
>>>   >  sessionInfo()
>>> R version 2.10.0 (2009-10-26)
>>> i386-pc-mingw32
>>>
>>> locale:
>>> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
>>> States.1252
>>> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>>>
>>> [5] LC_TIME=English_United States.1252
>>>
>>> attached base packages:
>>>    [1] grid      grDevices datasets  splines   graphics  stats
>>> tcltk
>>>       utils     methods
>>> [10] base
>>>
>>> other attached packages:
>>>    [1] made4_1.20.0         scatterplot3d_0.3-29 RColorBrewer_1.0-2
>>> ade4_1.4-14
>>>    [5] gplots_2.7.4         caTools_1.10         bitops_1.0-4.1
>>> gtools_2.6.1
>>>    [9] reshape_0.8.3        plyr_0.1.9           gdata_2.7.1
>>> svSocket_0.9-48
>>> [13] TinnR_1.0.3          R2HTML_1.59-1        Hmisc_3.7-0
>>> survival_2.35-7
>>>
>>> loaded via a namespace (and not attached):
>>> [1] cluster_1.12.1  lattice_0.17-26 svMisc_0.9-56   tools_2.10.0
>>>
>>>
>>>
>>> On 8/6/2010 7:34 PM, James W. MacDonald wrote:
>>>> Hi Karl,
>>>>
>>>> You need to show us the function call you used rather than saying what
>>>> you did. The errors indicate that you used the 'col' argument twice in
>>>> the first attempt and the 'dendrogram' argument twice in the second
>>>> attempt. But without seeing exactly what you did, nobody can say for
>>>> sure.
>>>>
>>>> Best,
>>>>
>>>> Jim
>>>>
>>>>
>>>>
>>>> On 8/6/10 11:55 AM, Karl Brand wrote:
>>>>> Esteemed BioC Users,
>>>>>
>>>>> Could some one help me obtain the garden variety microarray heatmap
>>>>> "red-*black*-green" palette in heatplot()? Using-
>>>>>
>>>>> lowcol="green", highcol="red"
>>>>>
>>>>> -has no black transition between red and green.
>>>>>
>>>>> Since its based on heatmap.2, i thought i could achieve this by
>>>>> passing the following argument to heatplot():
>>>>>
>>>>> cols.default=FASLE #to suppress default color palette
>>>>> col = c(redgreen(256))
>>>>>
>>>>> but get the error-
>>>>>
>>>>>> Error in heatmap.2(data, Colv = Colv, Rowv = Rowv, col = plotcols,
>>>>> scale = scale, :
>>>>>> formal argument "col" matched by multiple actual arguments
>>>>>
>>>>> I'd also like to suppress drawing of the row dendrogram (but NOT the
>>>>> reordering or rows), but again the heatmap.2 argument to do this-
>>>>>
>>>>> dendrogram = "column" #draw only column dendrograms
>>>>>
>>>>> returned-
>>>>>
>>>>>> Error in heatmap.2(data, Colv = Colv, Rowv = Rowv, col = plotcols,
>>>>> scale = scale, :
>>>>>> formal argument "dendrogram" matched by multiple actual arguments
>>>>>
>>>>> With thanks in advance, cheers,
>>>>>
>>>>> Karl
>>>>>
>>>>
>>>
>>> --
>>> Karl Brand
>>> Department of Genetics
>>> Erasmus MC
>>> Dr Molewaterplein 50
>>> 3015 GE Rotterdam
>>> T +31 (0)10 704 3457 |F +31 (0)10 704 4743 |M +31 (0)642 777 268
>>>
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>>>
>>
>>
>
> --
> Karl Brand
> Department of Genetics
> Erasmus MC
> Dr Molewaterplein 50
> 3015 GE Rotterdam
> T +31 (0)10 704 3457 |F +31 (0)10 704 4743 |M +31 (0)642 777 268
>