Question: Adding a text label to the classvec colour bar in heatplot
0
gravatar for Kasper Daniel Hansen
11.3 years ago by
United States
Kasper Daniel Hansen6.4k wrote:
It means you have a SVG device built into base R. So you can do svg() to open a SVG device. You do not need the package Thomas was talking about. This requires that R has been build with Cairo support, try R> capabilities() and look for "cairo". Kasper On Jul 27, 2008, at 2:24 PM, Mikhail, Amy wrote: > Hi Thomas and Kasper, > > Many thanks for the tip - I managed to carry out the adjustments I > needed in inkscape. I'd still reccomend adding a group label > feature to heatplot for general convenience, but modifying in svg > format does seem to be a very handy way of finalising things. > > Forgive my ignorance but what does "out of the box" mean (below)? > > Best wishes, > Amy > ________________________________________ > From: Kasper Daniel Hansen [khansen at stat.berkeley.edu] > Sent: 25 July 2008 20:31 > To: Thomas Girke > Cc: Mikhail, Amy; 'aedin at jimmy.harvard.edu'; bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Adding a text label to the classvec colour bar > in heatplot > > You will be glad to know that as of 2.7 R supports a SVG device out of > the box (if compiled with Cairo support). > > Kasper > > On Jul 25, 2008, at 8:38 AM, Thomas Girke wrote: > >> What I find often very helpful for the final refinements of a >> heatmaps or >> any other graphics generated in R is the possibility to save the >> plots >> in SVG format (Scalable Vector Graphics). This format allows you to >> edit all features in an R plot with graphics editors that have SVG >> support. >> A very nice and free one is InkScape: http://www.inkscape.org/. Adobe >> Illustrator should work too. After the import of the SVG file into >> InkScape you ungroup the graphics object to make all the changes >> final >> refinements you want. The SVG format is supported by many web >> browsers and >> it is becoming more and more the default graphics format for >> community >> web projects like Wikipedia. >> >> Here is a short example: >> >> library("RSvgDevice") # install package from CRAN >> devSVG("test.svg") >> plot(1:10, 1:10) >> dev.off() >> >> Thomas >> >> >> On Fri, Jul 25, 2008 at 01:06:28PM +0100, Mikhail, Amy wrote: >>> Hi Aedin, >>> >>> What I'd like to do is add group text labels over the colourbar on >>> the top (the rows in my heatplot are genes, the columns are >>> samples). If you look at figures 2 or 3 in the paper below which >>> is co-authored by Robert Gentleman you can see an example of what I >>> mean - the "Relapse" "CCR" labels on the 3rd figure are the type of >>> thing I'm after. This paper was written a while ago (2003) so not >>> sure if the figures were made with heatplot or something else, but >>> I'd be interested to know how it was done? >>> >>> http://bloodjournal.hematologylibrary.org/cgi/content/abstract/103 /7/2771 >>> >>> The dendrogram group labels are not quite what I'm after but it >>> would be interesting to see anyway. I think it would be useful if >>> heatplot had a straight-forward option to add group labels in this >>> way. >>> >>> Best wishes, >>> Amy >>> >>> -----Original Message----- >>> From: Aedin Culhane [mailto:aedin at jimmy.harvard.edu] >>> Sent: 25 July 2008 00:02 >>> To: bioconductor at stat.math.ethz.ch; Mikhail, Amy >>> Subject: Re: Adding a text label to the classvec colour bar in >>> heatplot >>> >>> Dear Amy >>> Do you want to add a group text label on each sample, or just over >>> the colorbar on the side ? The label on each sample is easy to >>> do. Do you want code for this? >>> >>> However currently I haven't implemented a group text label on >>> colorbars in heatplot. I don't think its available in heatmap or >>> heatmap.2. >>> >>> Another function, we have called pretty.dend draws multiple >>> colorbars beneath a clustering dendrogram and these colorbars have >>> group labels. >>> In the development version I used mtext to add the group labels to >>> the side of the color bar and this is prettier than the function >>> in the current release. >>> >>> Unfortunately I haven't implemented group labels adjacent to the >>> colorbar in heatplot as I would have to write code that doesn't >>> call heatmap/heatmap.2. >>> >>> Let me know if you find an alternative work around, or if you need >>> me to modify heatplot. >>> >>> I can send you the development version of pretty.dend so you can >>> see what the output looks like. The output from a modified version >>> of heatplot would look very similar (but has the option of >>> including a heatmap). >>> >>> Regards >>> Aedin >>> >>> (and.. BioC developers... I know I should modify pretty.dend so it >>> doesn't have a . in the function name... sorry, my mistake, its on >>> my to-do list ;-) >>> >>> >>> >>> Dear BioCs, >>> >>> I'm trying to create a heat plot with a matrix containing real time >>> PCR data for just 5 genes. There are 105 samples, belonging to 7 >>> groups (groups are in numerical order). The matrix looks like this >>> (Age is my grouping variable): >>> >>> Gene1 Gene2 Gene3 Gene4 >>> Gene5 Age >>> A1R_D03 -13.71434 -14.19288 -15.79439 -14.93712 -14.87174 3 >>> A4R_D03 -13.29068 -13.39888 -16.49077 -14.87276 -15.21852 3 >>> A7R_D03 -13.19423 -13.09508 -15.80787 -14.59671 -14.47190 3 >>> A10R_D03 -13.33472 -13.34051 -15.60396 -14.69521 -14.28135 3 >>> A13R_D03 -11.89260 -11.73026 -16.05069 -14.59895 -16.40680 3 >>> A61K_D03 -14.64341 -14.55358 -16.37900 -15.44644 -15.80778 3 >>> >>> ...etc >>> >>> As there are so many samples, it doesn't make sense to have the >>> individual sample names on the graph, so I would like to have the >>> samples in their group order with just the seven group labels. >>> With heatplot I can get the colourbar for my seven groups using the >>> classvec argument, but can't find any way to label the colourbars >>> with text... >>> >>> Also, I'm a little confused about the re-ordering that heatplot >>> does - how can I be sure that the samples belonging to a particular >>> group are underneath the appropriate colourbar (and given my >>> situation I would also want the groups to appear in numerical >>> order)? >>> >>> I have tried using heatmap.2 as well, but it seems only heatplot >>> has the colour bar by group option - heatmap.2 only allows you to >>> add a colourbar representing each column separately? >>> >>> Here is my code: >>> >>> #(Ngenet is a transposition of my matrix and the Age variable is in >>> a separate dataframe so that it doesn't appear directly on the >>> plot). >>> >>> >>>>> heatplot(Ngenet, dend="none", cols.default=FALSE, margin=c(7, 7), >>>>> labCol=FALSE, lowcol="red", highcol="green", scale="none", >>>>> classvec=Mop$Age) >>>> >>> >>> If anyone could suggest how I might add the group labels, I'd be >>> very grateful - appologies if this is something very simple, I have >>> actually seen papers with plots showing exactly what I want to do >>> but just can't figure out how to do it. >>> >>> With best wishes, >>> Amy >>> >>> >>> >>> >>> -- >>> Aed?n Culhane, >>> Research Associate >>> Computational Biology and Functional Genomics Laboratory Harvard >>> School of Public Health, Dana-Farber Cancer Institute >>> >>> 44 Binney Street, SM822C >>> Department of Biostatistics and Computational Biology, Dana-Farber >>> Cancer Institute Boston, MA 02115 USA >>> >>> Phone: +1 (617) 632 2468 >>> Fax: +1 (617) 582 7760 >>> Email: aedin at jimmy.harvard.edu >>> Web URL: http://www.hsph.harvard.edu/researchers/aculhane.html >>> >>> >>> >>> >>> The University of Aberdeen is a charity registered in Scotland, No >>> SC013683. >>> >>> _______________________________________________ >>> 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 >>> >> >> -- >> Thomas Girke >> Assistant Professor of Bioinformatics >> Director, IIGB Bioinformatic Facility >> Center for Plant Cell Biology (CEPCEB) >> Institute for Integrative Genome Biology (IIGB) >> Department of Botany and Plant Sciences >> 1008 Noel T. Keen Hall >> University of California >> Riverside, CA 92521 >> >> E-mail: thomas.girke at ucr.edu >> Website: http://faculty.ucr.edu/~tgirke >> Ph: 951-827-2469 >> Fax: 951-827-4437 >> >> _______________________________________________ >> 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 > > > > The University of Aberdeen is a charity registered in Scotland, No > SC013683.
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ADD COMMENTlink modified 11.3 years ago by Amy Mikhail460 • written 11.3 years ago by Kasper Daniel Hansen6.4k
Answer: Adding a text label to the classvec colour bar in heatplot
0
gravatar for Amy Mikhail
11.3 years ago by
Amy Mikhail460
Amy Mikhail460 wrote:
Hi Kasper, Thanks for the explanation... I looked for Cairo in the capabilities as you suggested, and it says "FALSE". That is with R 2.7.1 on a windows xp operating system - is building with Cairo support something you can choose during the install or does this really only apply if you build R from source? > capabilities() jpeg png tcltk X11 aqua http/ftp sockets libxml fifo cledit iconv NLS TRUE TRUE TRUE FALSE FALSE TRUE TRUE TRUE FALSE TRUE TRUE TRUE profmem cairo FALSE FALSE > svg() Error: could not find function "svg" > sessionInfo() R version 2.7.1 (2008-06-23) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.7.1 With best wishes, Amy ________________________________________. From: Kasper Daniel Hansen [khansen@stat.berkeley.edu] Sent: 01 August 2008 06:25 To: Mikhail, Amy Cc: Thomas Girke; 'aedin at jimmy.harvard.edu'; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Adding a text label to the classvec colour bar in heatplot It means you have a SVG device built into base R. So you can do svg() to open a SVG device. You do not need the package Thomas was talking about. This requires that R has been build with Cairo support, try R> capabilities() and look for "cairo". Kasper On Jul 27, 2008, at 2:24 PM, Mikhail, Amy wrote: > Hi Thomas and Kasper, > > Many thanks for the tip - I managed to carry out the adjustments I > needed in inkscape. I'd still reccomend adding a group label > feature to heatplot for general convenience, but modifying in svg > format does seem to be a very handy way of finalising things. > > Forgive my ignorance but what does "out of the box" mean (below)? > > Best wishes, > Amy > ________________________________________ > From: Kasper Daniel Hansen [khansen at stat.berkeley.edu] > Sent: 25 July 2008 20:31 > To: Thomas Girke > Cc: Mikhail, Amy; 'aedin at jimmy.harvard.edu'; bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Adding a text label to the classvec colour bar > in heatplot > > You will be glad to know that as of 2.7 R supports a SVG device out of > the box (if compiled with Cairo support). > > Kasper > > On Jul 25, 2008, at 8:38 AM, Thomas Girke wrote: > >> What I find often very helpful for the final refinements of a >> heatmaps or >> any other graphics generated in R is the possibility to save the >> plots >> in SVG format (Scalable Vector Graphics). This format allows you to >> edit all features in an R plot with graphics editors that have SVG >> support. >> A very nice and free one is InkScape: http://www.inkscape.org/. Adobe >> Illustrator should work too. After the import of the SVG file into >> InkScape you ungroup the graphics object to make all the changes >> final >> refinements you want. The SVG format is supported by many web >> browsers and >> it is becoming more and more the default graphics format for >> community >> web projects like Wikipedia. >> >> Here is a short example: >> >> library("RSvgDevice") # install package from CRAN >> devSVG("test.svg") >> plot(1:10, 1:10) >> dev.off() >> >> Thomas >> >> >> On Fri, Jul 25, 2008 at 01:06:28PM +0100, Mikhail, Amy wrote: >>> Hi Aedin, >>> >>> What I'd like to do is add group text labels over the colourbar on >>> the top (the rows in my heatplot are genes, the columns are >>> samples). If you look at figures 2 or 3 in the paper below which >>> is co-authored by Robert Gentleman you can see an example of what I >>> mean - the "Relapse" "CCR" labels on the 3rd figure are the type of >>> thing I'm after. This paper was written a while ago (2003) so not >>> sure if the figures were made with heatplot or something else, but >>> I'd be interested to know how it was done? >>> >>> http://bloodjournal.hematologylibrary.org/cgi/content/abstract/103 /7/2771 >>> >>> The dendrogram group labels are not quite what I'm after but it >>> would be interesting to see anyway. I think it would be useful if >>> heatplot had a straight-forward option to add group labels in this >>> way. >>> >>> Best wishes, >>> Amy >>> >>> -----Original Message----- >>> From: Aedin Culhane [mailto:aedin at jimmy.harvard.edu] >>> Sent: 25 July 2008 00:02 >>> To: bioconductor at stat.math.ethz.ch; Mikhail, Amy >>> Subject: Re: Adding a text label to the classvec colour bar in >>> heatplot >>> >>> Dear Amy >>> Do you want to add a group text label on each sample, or just over >>> the colorbar on the side ? The label on each sample is easy to >>> do. Do you want code for this? >>> >>> However currently I haven't implemented a group text label on >>> colorbars in heatplot. I don't think its available in heatmap or >>> heatmap.2. >>> >>> Another function, we have called pretty.dend draws multiple >>> colorbars beneath a clustering dendrogram and these colorbars have >>> group labels. >>> In the development version I used mtext to add the group labels to >>> the side of the color bar and this is prettier than the function >>> in the current release. >>> >>> Unfortunately I haven't implemented group labels adjacent to the >>> colorbar in heatplot as I would have to write code that doesn't >>> call heatmap/heatmap.2. >>> >>> Let me know if you find an alternative work around, or if you need >>> me to modify heatplot. >>> >>> I can send you the development version of pretty.dend so you can >>> see what the output looks like. The output from a modified version >>> of heatplot would look very similar (but has the option of >>> including a heatmap). >>> >>> Regards >>> Aedin >>> >>> (and.. BioC developers... I know I should modify pretty.dend so it >>> doesn't have a . in the function name... sorry, my mistake, its on >>> my to-do list ;-) >>> >>> >>> >>> Dear BioCs, >>> >>> I'm trying to create a heat plot with a matrix containing real time >>> PCR data for just 5 genes. There are 105 samples, belonging to 7 >>> groups (groups are in numerical order). The matrix looks like this >>> (Age is my grouping variable): >>> >>> Gene1 Gene2 Gene3 Gene4 >>> Gene5 Age >>> A1R_D03 -13.71434 -14.19288 -15.79439 -14.93712 -14.87174 3 >>> A4R_D03 -13.29068 -13.39888 -16.49077 -14.87276 -15.21852 3 >>> A7R_D03 -13.19423 -13.09508 -15.80787 -14.59671 -14.47190 3 >>> A10R_D03 -13.33472 -13.34051 -15.60396 -14.69521 -14.28135 3 >>> A13R_D03 -11.89260 -11.73026 -16.05069 -14.59895 -16.40680 3 >>> A61K_D03 -14.64341 -14.55358 -16.37900 -15.44644 -15.80778 3 >>> >>> ...etc >>> >>> As there are so many samples, it doesn't make sense to have the >>> individual sample names on the graph, so I would like to have the >>> samples in their group order with just the seven group labels. >>> With heatplot I can get the colourbar for my seven groups using the >>> classvec argument, but can't find any way to label the colourbars >>> with text... >>> >>> Also, I'm a little confused about the re-ordering that heatplot >>> does - how can I be sure that the samples belonging to a particular >>> group are underneath the appropriate colourbar (and given my >>> situation I would also want the groups to appear in numerical >>> order)? >>> >>> I have tried using heatmap.2 as well, but it seems only heatplot >>> has the colour bar by group option - heatmap.2 only allows you to >>> add a colourbar representing each column separately? >>> >>> Here is my code: >>> >>> #(Ngenet is a transposition of my matrix and the Age variable is in >>> a separate dataframe so that it doesn't appear directly on the >>> plot). >>> >>> >>>>> heatplot(Ngenet, dend="none", cols.default=FALSE, margin=c(7, 7), >>>>> labCol=FALSE, lowcol="red", highcol="green", scale="none", >>>>> classvec=Mop$Age) >>>> >>> >>> If anyone could suggest how I might add the group labels, I'd be >>> very grateful - appologies if this is something very simple, I have >>> actually seen papers with plots showing exactly what I want to do >>> but just can't figure out how to do it. >>> >>> With best wishes, >>> Amy >>> >>> >>> >>> >>> -- >>> Aed?n Culhane, >>> Research Associate >>> Computational Biology and Functional Genomics Laboratory Harvard >>> School of Public Health, Dana-Farber Cancer Institute >>> >>> 44 Binney Street, SM822C >>> Department of Biostatistics and Computational Biology, Dana-Farber >>> Cancer Institute Boston, MA 02115 USA >>> >>> Phone: +1 (617) 632 2468 >>> Fax: +1 (617) 582 7760 >>> Email: aedin at jimmy.harvard.edu >>> Web URL: http://www.hsph.harvard.edu/researchers/aculhane.html >>> >>> >>> >>> >>> The University of Aberdeen is a charity registered in Scotland, No >>> SC013683. >>> >>> _______________________________________________ >>> 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 >>> >> >> -- >> Thomas Girke >> Assistant Professor of Bioinformatics >> Director, IIGB Bioinformatic Facility >> Center for Plant Cell Biology (CEPCEB) >> Institute for Integrative Genome Biology (IIGB) >> Department of Botany and Plant Sciences >> 1008 Noel T. Keen Hall >> University of California >> Riverside, CA 92521 >> >> E-mail: thomas.girke at ucr.edu >> Website: http://faculty.ucr.edu/~tgirke >> Ph: 951-827-2469 >> Fax: 951-827-4437 >> >> _______________________________________________ >> 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 > > > > The University of Aberdeen is a charity registered in Scotland, No > SC013683. The University of Aberdeen is a charity registered in Scotland, No SC013683.
ADD COMMENTlink written 11.3 years ago by Amy Mikhail460
Builing R with cairo suport is something you do when you compile R from scratch, so it will be very hard for you to fix the "problem". I don't know much about Cairo (which is a set of graphics tools), but I assume that it has been hard to get to work under WIndows. I am not really following the R for windows scene, but I was surprised to see that R-2.7.1 for Windows did not have SVG support. In that case, using the package that Thomas recommends, makes a lot of sense (= being the only relevant solution). Kasper On Aug 1, 2008, at 5:05 AM, Mikhail, Amy wrote: > Hi Kasper, > > Thanks for the explanation... I looked for Cairo in the capabilities > as you suggested, and it says "FALSE". That is with R 2.7.1 on a > windows xp operating system - is building with Cairo support > something you can choose during the install or does this really only > apply if you build R from source? > >> capabilities() > jpeg png tcltk X11 aqua http/ftp sockets > libxml fifo cledit iconv NLS > TRUE TRUE TRUE FALSE FALSE TRUE TRUE > TRUE FALSE TRUE TRUE TRUE > profmem cairo > FALSE FALSE > >> svg() > Error: could not find function "svg" > >> sessionInfo() > R version 2.7.1 (2008-06-23) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > Kingdom.1252;LC_MONETARY=English_United Kingdom. > 1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tools_2.7.1 > > > With best wishes, > Amy > ________________________________________. > From: Kasper Daniel Hansen [khansen at stat.berkeley.edu] > Sent: 01 August 2008 06:25 > To: Mikhail, Amy > Cc: Thomas Girke; 'aedin at jimmy.harvard.edu'; bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Adding a text label to the classvec colour bar > in heatplot > > It means you have a SVG device built into base R. So you can do > > svg() > > to open a SVG device. You do not need the package Thomas was talking > about. This requires that R has been build with Cairo support, try > R> capabilities() > and look for "cairo". > > Kasper > > > On Jul 27, 2008, at 2:24 PM, Mikhail, Amy wrote: > >> Hi Thomas and Kasper, >> >> Many thanks for the tip - I managed to carry out the adjustments I >> needed in inkscape. I'd still reccomend adding a group label >> feature to heatplot for general convenience, but modifying in svg >> format does seem to be a very handy way of finalising things. >> >> Forgive my ignorance but what does "out of the box" mean (below)? >> >> Best wishes, >> Amy >> ________________________________________ >> From: Kasper Daniel Hansen [khansen at stat.berkeley.edu] >> Sent: 25 July 2008 20:31 >> To: Thomas Girke >> Cc: Mikhail, Amy; 'aedin at jimmy.harvard.edu'; bioconductor at stat.math.ethz.ch >> Subject: Re: [BioC] Adding a text label to the classvec colour bar >> in heatplot >> >> You will be glad to know that as of 2.7 R supports a SVG device out >> of >> the box (if compiled with Cairo support). >> >> Kasper >> >> On Jul 25, 2008, at 8:38 AM, Thomas Girke wrote: >> >>> What I find often very helpful for the final refinements of a >>> heatmaps or >>> any other graphics generated in R is the possibility to save the >>> plots >>> in SVG format (Scalable Vector Graphics). This format allows you to >>> edit all features in an R plot with graphics editors that have SVG >>> support. >>> A very nice and free one is InkScape: http://www.inkscape.org/. >>> Adobe >>> Illustrator should work too. After the import of the SVG file into >>> InkScape you ungroup the graphics object to make all the changes >>> final >>> refinements you want. The SVG format is supported by many web >>> browsers and >>> it is becoming more and more the default graphics format for >>> community >>> web projects like Wikipedia. >>> >>> Here is a short example: >>> >>> library("RSvgDevice") # install package from CRAN >>> devSVG("test.svg") >>> plot(1:10, 1:10) >>> dev.off() >>> >>> Thomas >>> >>> >>> On Fri, Jul 25, 2008 at 01:06:28PM +0100, Mikhail, Amy wrote: >>>> Hi Aedin, >>>> >>>> What I'd like to do is add group text labels over the colourbar on >>>> the top (the rows in my heatplot are genes, the columns are >>>> samples). If you look at figures 2 or 3 in the paper below which >>>> is co-authored by Robert Gentleman you can see an example of what I >>>> mean - the "Relapse" "CCR" labels on the 3rd figure are the type of >>>> thing I'm after. This paper was written a while ago (2003) so not >>>> sure if the figures were made with heatplot or something else, but >>>> I'd be interested to know how it was done? >>>> >>>> http://bloodjournal.hematologylibrary.org/cgi/content/abstract/10 3/7/2771 >>>> >>>> The dendrogram group labels are not quite what I'm after but it >>>> would be interesting to see anyway. I think it would be useful if >>>> heatplot had a straight-forward option to add group labels in this >>>> way. >>>> >>>> Best wishes, >>>> Amy >>>> >>>> -----Original Message----- >>>> From: Aedin Culhane [mailto:aedin at jimmy.harvard.edu] >>>> Sent: 25 July 2008 00:02 >>>> To: bioconductor at stat.math.ethz.ch; Mikhail, Amy >>>> Subject: Re: Adding a text label to the classvec colour bar in >>>> heatplot >>>> >>>> Dear Amy >>>> Do you want to add a group text label on each sample, or just over >>>> the colorbar on the side ? The label on each sample is easy to >>>> do. Do you want code for this? >>>> >>>> However currently I haven't implemented a group text label on >>>> colorbars in heatplot. I don't think its available in heatmap or >>>> heatmap.2. >>>> >>>> Another function, we have called pretty.dend draws multiple >>>> colorbars beneath a clustering dendrogram and these colorbars have >>>> group labels. >>>> In the development version I used mtext to add the group labels to >>>> the side of the color bar and this is prettier than the function >>>> in the current release. >>>> >>>> Unfortunately I haven't implemented group labels adjacent to the >>>> colorbar in heatplot as I would have to write code that doesn't >>>> call heatmap/heatmap.2. >>>> >>>> Let me know if you find an alternative work around, or if you need >>>> me to modify heatplot. >>>> >>>> I can send you the development version of pretty.dend so you can >>>> see what the output looks like. The output from a modified version >>>> of heatplot would look very similar (but has the option of >>>> including a heatmap). >>>> >>>> Regards >>>> Aedin >>>> >>>> (and.. BioC developers... I know I should modify pretty.dend so it >>>> doesn't have a . in the function name... sorry, my mistake, its on >>>> my to-do list ;-) >>>> >>>> >>>> >>>> Dear BioCs, >>>> >>>> I'm trying to create a heat plot with a matrix containing real time >>>> PCR data for just 5 genes. There are 105 samples, belonging to 7 >>>> groups (groups are in numerical order). The matrix looks like this >>>> (Age is my grouping variable): >>>> >>>> Gene1 Gene2 Gene3 Gene4 >>>> Gene5 Age >>>> A1R_D03 -13.71434 -14.19288 -15.79439 -14.93712 -14.87174 3 >>>> A4R_D03 -13.29068 -13.39888 -16.49077 -14.87276 -15.21852 3 >>>> A7R_D03 -13.19423 -13.09508 -15.80787 -14.59671 -14.47190 3 >>>> A10R_D03 -13.33472 -13.34051 -15.60396 -14.69521 -14.28135 3 >>>> A13R_D03 -11.89260 -11.73026 -16.05069 -14.59895 -16.40680 3 >>>> A61K_D03 -14.64341 -14.55358 -16.37900 -15.44644 -15.80778 3 >>>> >>>> ...etc >>>> >>>> As there are so many samples, it doesn't make sense to have the >>>> individual sample names on the graph, so I would like to have the >>>> samples in their group order with just the seven group labels. >>>> With heatplot I can get the colourbar for my seven groups using the >>>> classvec argument, but can't find any way to label the colourbars >>>> with text... >>>> >>>> Also, I'm a little confused about the re-ordering that heatplot >>>> does - how can I be sure that the samples belonging to a particular >>>> group are underneath the appropriate colourbar (and given my >>>> situation I would also want the groups to appear in numerical >>>> order)? >>>> >>>> I have tried using heatmap.2 as well, but it seems only heatplot >>>> has the colour bar by group option - heatmap.2 only allows you to >>>> add a colourbar representing each column separately? >>>> >>>> Here is my code: >>>> >>>> #(Ngenet is a transposition of my matrix and the Age variable is in >>>> a separate dataframe so that it doesn't appear directly on the >>>> plot). >>>> >>>> >>>>>> heatplot(Ngenet, dend="none", cols.default=FALSE, margin=c(7, 7), >>>>>> labCol=FALSE, lowcol="red", highcol="green", scale="none", >>>>>> classvec=Mop$Age) >>>>> >>>> >>>> If anyone could suggest how I might add the group labels, I'd be >>>> very grateful - appologies if this is something very simple, I have >>>> actually seen papers with plots showing exactly what I want to do >>>> but just can't figure out how to do it. >>>> >>>> With best wishes, >>>> Amy >>>> >>>> >>>> >>>> >>>> -- >>>> Aed?n Culhane, >>>> Research Associate >>>> Computational Biology and Functional Genomics Laboratory Harvard >>>> School of Public Health, Dana-Farber Cancer Institute >>>> >>>> 44 Binney Street, SM822C >>>> Department of Biostatistics and Computational Biology, Dana- Farber >>>> Cancer Institute Boston, MA 02115 USA >>>> >>>> Phone: +1 (617) 632 2468 >>>> Fax: +1 (617) 582 7760 >>>> Email: aedin at jimmy.harvard.edu >>>> Web URL: http://www.hsph.harvard.edu/researchers/aculhane.html >>>> >>>> >>>> >>>> >>>> The University of Aberdeen is a charity registered in Scotland, No >>>> SC013683. >>>> >>>> _______________________________________________ >>>> 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 >>>> >>> >>> -- >>> Thomas Girke >>> Assistant Professor of Bioinformatics >>> Director, IIGB Bioinformatic Facility >>> Center for Plant Cell Biology (CEPCEB) >>> Institute for Integrative Genome Biology (IIGB) >>> Department of Botany and Plant Sciences >>> 1008 Noel T. Keen Hall >>> University of California >>> Riverside, CA 92521 >>> >>> E-mail: thomas.girke at ucr.edu >>> Website: http://faculty.ucr.edu/~tgirke >>> Ph: 951-827-2469 >>> Fax: 951-827-4437 >>> >>> _______________________________________________ >>> 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 >> >> >> >> The University of Aberdeen is a charity registered in Scotland, No >> SC013683. > > > > The University of Aberdeen is a charity registered in Scotland, No > SC013683.
ADD REPLYlink written 11.3 years ago by Kasper Daniel Hansen6.4k
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