Hi Catalina,
The error message is pretty clear. min(diff(breaks)/100) evaluates to
a negative number. Perhaps the sort order for the values in "breaks"
has changed.
Jim
On Tue, Apr 19, 2016 at 9:35 AM, Catalina Aguilar Hurtado
<cata...@gmail.com> wrote:
> Hi I am trying to understand what happen with the heatmap.2 code that it
> used to work (last used in October 2015). I am able to get a heatmap but my
> colour key doesn't come up and instead I get an error in all my files the
> used to work. Does anyone has any idea of what could have changed? or how
> to fix this.
>
> Thanks.
>
> #
>
> Error in seq.default(min.raw, max.raw, by = min(diff(breaks)/100)) :
> wrong sign in 'by' argument
> In addition: Warning message:
> In image.default(1:nc, 1:nr, x, xlim = 0.5 + c(0, nc), ylim = 0.5 + :
> unsorted 'breaks' will be sorted before use
>
> ##
>
> library("RColorBrewer")
> library("gplots")
>
> library ("gtools")
>
> GO_Fil=read.table("1h-6h-up-down-v4.csv", sep=",", header=T)
>
> data =data.matrix (GO_Fil[,3:4]) # define which columns to use for the
> heatmap
>
> rownames(data) <- GO_Fil$Description
>
> summary (data)
>
> pairs.breaks <- c(seq(-6, -0.01, length.out=50), seq(-0.02,
> 0.01,length.out=150), seq(0.02, 3.9,length.out=80))
>
> hmcols<- colorRampPalette(c("blue","white", "red"))(length(pairs.breaks)-1)
>
> pdf("Heat_1hv6h-updown-key.pdf",
> width = 15,
> height = 20,
> pointsize = 5)
>
> hm<- heatmap.2(data, breaks=pairs.breaks, col=hmcols, na.color="white",
> trace="none",Colv=FALSE,
> dendrogram = "none",
> density.info="none",
> key="TRUE",
> keysize = 2,
> key.xlab = "Log2FC",
> key.title = "key",
> cexCol=3.0,
> cexRow=2,
> lwid= c(0.4,1),
> lhei = c(0.1, 4),
> margins= c(50,80),
> symm=F,symkey=F,symbreaks=T, scale="none")
>
> dev.off()
>
>> R.version
> _
> platform x86_64-apple-darwin13.4.0
> arch x86_64
> os darwin13.4.0
> system x86_64, darwin13.4.0
> status
> major 3
> minor 2.2
> year 2015
> month 08
> day 14
> svn rev 69053
> language R
> version.string R version 3.2.2 (2015-08-14)
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
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> and provide commented, minimal, self-contained, reproducible code.
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