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

[Karl Brand]

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