[R] heatmap2 error key

[John Kane]

Data?  Please have a look at
http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example and/or http://adv-r.had.co.nz/Reproducibility.html



John Kane
Kingston ON Canada


> -----Original Message-----
> From: catagui at gmail.com
> Sent: Tue, 19 Apr 2016 09:35:14 +1000
> To: r-help at r-project.org
> Subject: [R] heatmap2 error key
> 
> 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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