How to use Negative values as gene density values when using RIdeogram?
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Hi, I'm trying to use DEG data for an ideogram plot, but it seems the gene_density should be between 1 and 10000 (cnum <- 10000 in the origin code). Negative values were not counted?
Any suggestions will be greatly appreciated!
Script:
mouse_karyotype <- read.table("mouse_karyotype.txt", sep = "\t", header = T, stringsAsFactors = F)
gene_density <- read.table("DensityA.txt", sep = "\t", header = T, stringsAsFactors = F)
str(gene_density)
'data.frame': 422 obs. of 4 variables:
$ Chr : chr "10" "17" "19" "5" ...
$ Start: int 80805018 50279393 46667165 67607883 25466709 98842356 98354245 133350674 85684267 152576086 ...
$ End : int 80807648 50293620 46673000 67613987 25470113 98859789 98356705 133360320 85688254 152580312 ...
$ value: num 7.75 6.54 8.25 -5.57 6.71 ...
ideogram(karyotype = mouse_karyotype)
ideogram(karyotype = mouse_karyotype, overlaid = gene_density)
Error in round(rescale(mydata$Value, to = c(1, cnum))) :
non-numeric argument to mathematical function