Pijush,
The error is a result of you having repeated color values. The warnings
can be addressed by changing the arguments that you use. Attachments are
removed from posts to R Help, so I used different data to show you an
example.
Jean
library(gplots)
data(mtcars)
x <- as.matrix(mtcars[1:6, 3:4])
x[1:3, ] <- -x[1:3, ]
colors1 <- c(seq(-170, 0, 10), seq(0, 370, 10))
my_palette1 <- colorRampPalette(c("green", "black",
"red"))(n=length(colors1)-1)
heatmap.2(x, col=my_palette1, breaks=colors1, symkey=FALSE, density.info
="none",
trace="none", dendrogram="none")
colors2 <- unique(colors1)
my_palette2 <- colorRampPalette(c("green", "black",
"red"))(n=length(colors2)-1)
heatmap.2(x, col=my_palette2, breaks=colors2, symkey=FALSE, density.info
="none",
trace="none", dendrogram="none")
On Fri, Jun 19, 2015 at 9:02 AM, Pijush Das <topijush at gmail.com> wrote:
> Dear Sir,
>
> Please help me solving the error occurring during the execution of the code
> given below.
>
>
> library("openxlsx")
> library(gplots)
> library("RColorBrewer")
>
> rix <- read.xlsx(file.choose(), sheet = 1, colNames = TRUE,rowNames =
TRUE)
> rawdata <- data.matrix(rix)
>
>
> colors >
c(seq(-2,-0.5,length=100),seq(-0.5,1,length=100),seq(1,2,length=100))
> my_palette <- colorRampPalette(c("green", "black",
"red"))(n = 299)
>
> heatmap.2(rawdata, col=my_palette, scale="row", key=TRUE,
symkey=FALSE,
> density.info="none", trace="none", cexRow=0.5, Rowv =
FALSE, Colv=FALSE,
> breaks=colors)
>
>
> Error in seq.default(min.raw, max.raw, by = min(diff(breaks)/4)) : invalid
> (to - from)/by in seq(.)
> In addition: Warning messages:
> 1: In heatmap.2(rawdata, col = my_palette, scale = "row", key =
TRUE, :
> Using scale="row" or scale="column" when breaks
arespecified can produce
> unpredictable results.Please consider using only one or the other.
> 2: In heatmap.2(rawdata, col = my_palette, scale = "row", key =
TRUE, :
> Discrepancy: Rowv is FALSE, while dendrogram is `none'. Omitting row
> dendogram.
> >
>
> Please find the data set attached with the email.
>
>
> Thanking you.
>
> Regards
> Pijush
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