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)
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