Hi When I give the command:>heatmap.2(as.matrix(d),Rowv=as.dendrogram(hc.gene),Colv=FALSE,scale="row ",trace="none",col=greenred.colors(79)) The resulting heatmap has re-ordered my columns! This is time-course data, and I don't want my columns re-ordered! Note from the help: Rowv: determines if and how the _row_ dendrogram should be reordered. Either a 'dendrogram' or a vector of values used to reorder the row dendrogram or 'FALSE' to suppress reordering or by default, 'NULL', see _Details_ below. Colv: determines if and how the _column_ dendrogram should be reordered. Has the options as the 'Rowv' argument above and _additionally_ when 'x' is a square matrix, 'Colv = "Rowv"' means that columns should be treated identically to the rows. I have specifically set "Colv=FALSE" in my command. Help? What am I doing wrong? Cheers Mick
Didn't test this, but I think you probably want to do dendrogram="row",Colv=1:n where n is the number of samples. Sean On Sep 2, 2004, at 9:21 AM, michael watson (IAH-C) wrote:> Hi > > When I give the command: > >> > heatmap.2(as.matrix(d),Rowv=as.dendrogram(hc.gene),Colv=FALSE,scale="ro > w > ",trace="none",col=greenred.colors(79)) > > The resulting heatmap has re-ordered my columns! This is time-course > data, and I don't want my columns re-ordered! Note from the help: > > Rowv: determines if and how the _row_ dendrogram should be > reordered. Either a 'dendrogram' or a vector of values used > to reorder the row dendrogram or 'FALSE' to suppress > reordering or by default, 'NULL', see _Details_ below. > > Colv: determines if and how the _column_ dendrogram should be > reordered. Has the options as the 'Rowv' argument above and > _additionally_ when 'x' is a square matrix, 'Colv = "Rowv"' > means that columns should be treated identically to the rows. > > I have specifically set "Colv=FALSE" in my command. > > Help? What am I doing wrong? > > Cheers > Mick > > ______________________________________________ > 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
Hi I'm afraid not! heatmap.2(as.matrix(d),Rowv=as.dendrogram(hc.gene),Colv=1:4,scale="row", trace="none",col=greenred.colors(79)) Produces exactly the same results as if "Colv=FALSE" - my columns get re-ordered (by a dendrogram no less). Clearly this isn't meant to be happening.... (by the way, d is NOT a square matrix either) Cheers Mick -----Original Message----- From: Sean Davis [mailto:sdavis2 at mail.nih.gov] Sent: 02 September 2004 14:39 To: michael watson (IAH-C) Cc: r-help at stat.math.ethz.ch Subject: Re: [R] Problems with heatmap.2 Didn't test this, but I think you probably want to do dendrogram="row",Colv=1:n where n is the number of samples. Sean On Sep 2, 2004, at 9:21 AM, michael watson (IAH-C) wrote:> Hi > > When I give the command: > >> > heatmap.2(as.matrix(d),Rowv=as.dendrogram(hc.gene),Colv=FALSE,scale="r > o > w > ",trace="none",col=greenred.colors(79)) > > The resulting heatmap has re-ordered my columns! This is time-course > data, and I don't want my columns re-ordered! Note from the help: > > Rowv: determines if and how the _row_ dendrogram should be > reordered. Either a 'dendrogram' or a vector of values used > to reorder the row dendrogram or 'FALSE' to suppress > reordering or by default, 'NULL', see _Details_ below. > > Colv: determines if and how the _column_ dendrogram should be > reordered. Has the options as the 'Rowv' argument above and > _additionally_ when 'x' is a square matrix, 'Colv = "Rowv"' > means that columns should be treated identically to the > rows. > > I have specifically set "Colv=FALSE" in my command. > > Help? What am I doing wrong? > > Cheers > Mick > > ______________________________________________ > 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
Ploughing on and solving my own problem, I find that setting: dendrogram="row" In heatmap.2 swicthes off column ordering. Except that column ordering should have been switched off anyway, by Colv=FALSE, shouldn't it? Oh and "dendrogram" is spelled "dendogram" in the help :-) Now all I need to know is how to switch off that damn histogram.... :-D Mick -----Original Message----- From: michael watson (IAH-C) Sent: 03 September 2004 10:00 To: Sean Davis Cc: r-help at stat.math.ethz.ch Subject: RE: [R] Problems with heatmap.2 Hi I'm afraid not! heatmap.2(as.matrix(d),Rowv=as.dendrogram(hc.gene),Colv=1:4,scale="row", trace="none",col=greenred.colors(79)) Produces exactly the same results as if "Colv=FALSE" - my columns get re-ordered (by a dendrogram no less). Clearly this isn't meant to be happening.... (by the way, d is NOT a square matrix either) Cheers Mick -----Original Message----- From: Sean Davis [mailto:sdavis2 at mail.nih.gov] Sent: 02 September 2004 14:39 To: michael watson (IAH-C) Cc: r-help at stat.math.ethz.ch Subject: Re: [R] Problems with heatmap.2 Didn't test this, but I think you probably want to do dendrogram="row",Colv=1:n where n is the number of samples. Sean On Sep 2, 2004, at 9:21 AM, michael watson (IAH-C) wrote:> Hi > > When I give the command: > >> > heatmap.2(as.matrix(d),Rowv=as.dendrogram(hc.gene),Colv=FALSE,scale="r > o > w > ",trace="none",col=greenred.colors(79)) > > The resulting heatmap has re-ordered my columns! This is time-course > data, and I don't want my columns re-ordered! Note from the help: > > Rowv: determines if and how the _row_ dendrogram should be > reordered. Either a 'dendrogram' or a vector of values used > to reorder the row dendrogram or 'FALSE' to suppress > reordering or by default, 'NULL', see _Details_ below. > > Colv: determines if and how the _column_ dendrogram should be > reordered. Has the options as the 'Rowv' argument above and > _additionally_ when 'x' is a square matrix, 'Colv = "Rowv"' > means that columns should be treated identically to the > rows. > > I have specifically set "Colv=FALSE" in my command. > > Help? What am I doing wrong? > > Cheers > Mick > > ______________________________________________ > 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______________________________________________ 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