heatplot() 1. red-*black*-green palette, 2.suppress drawing of the row dendrogram (but NOT row reordering)
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k. brand ▴ 420
@k-brand-1874
Last seen 9.9 years ago
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 <k.brand at="" erasmusmc.nl=""> Department of Genetics Erasmus MC Dr Molewaterplein 50 3015 GE Rotterdam P +31 (0)10 704 3409 | F +31 (0)10 704 4743 | M +31 (0)642 777 268
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@james-w-macdonald-5106
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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 > -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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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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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 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. 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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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. *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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- 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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> 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 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> > > -- > 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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Hi Heidi, That's *exactly* what i wanted- an example of how to adjust these major aspects of a heat map, which i hope will help biologists in the future attempting this. Additionally the actual metrics are precisely what my data appear to 'like'. But i still cant move over to heatmap.2 having discovered the usefulness of heatplot's "dualScale=" argument which really 'tames' one or two outlying samples in my data (but may ultimately be discarded). And the "zlim=" arg is also very convenient. Both absent in heatmap.2 and too complex for me to 'port' them to heatmap.2 . I did also successfully mod heatplot() to use any 3 colors by replacing the following line in heatplot: hmcol <- colorRampPalette(brewer.pal(10, "RdBu"))(256) with, eg: hmcol <- redgreen(256) #To yield the red/black/green or, per your suggestion: hmcol <- colorpanel(256, "blue", "black", "yellow") So for now, its heatplot with the unwanted row dendrogram, or heatmap without the additional row & column scaling. Thanks again for your help, really appreciated, karl On 8/8/2010 9:51 PM, Heidi Dvinge wrote: >> 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 >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >>> >> >> -- >> 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 >> > > -- Karl Brand <k.brand at="" erasmusmc.nl=""> Department of Genetics Erasmus MC Dr Molewaterplein 50 3015 GE Rotterdam P +31 (0)10 704 3409 | F +31 (0)10 704 4743 | M +31 (0)642 777 268
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