Closed juancresc closed 4 years ago
I've tried the following with this karyotype file:
devtools::install_github('TickingClock1992/RIdeogram') require(RIdeogram) setwd('/home/juan/Desktop/juan/bio/svevo-zavitan') data(human_karyotype, package="RIdeogram") data(gene_density, package="RIdeogram") human_karyotype gene_density karyo = read.csv(file="data/karyotype.csv", header=TRUE, sep=",") density = read.csv(file="data/snp_dens.csv", header=TRUE, sep=",") ideogram(karyotype = karyo, overlaid = density) convertSVG("chromosome.svg", device = "png")
Chr,Start,End,CE_start,CE_end chr1A,0,585266722,0,0 chr1B,0,681112512,0,0 chr2A,0,775448786,0,0 chr2B,0,790338525,0,0 chr3A,0,746673839,0,0 chr3B,0,836514780,0,0 chr4A,0,736872137,0,0 chr4B,0,676292951,0,0 chr5A,0,669155517,0,0 chr5B,0,701372996,0,0 chr6A,0,615672275,0,0 chr6B,0,698614761,0,0 chr7A,0,728031845,0,0 chr7B,0,722970987,0,0 chrUn,0,498719471,0,0
and got the following error:
ideogram(karyotype = karyo, overlaid = density) Error in nchar(karyotype$Chr) : 'nchar()' requires a character vector
So I have to modify my karyotype as follow:
Chr,Start,End,CE_start,CE_end 1,0,585266722,0,0 2,0,681112512,0,0 3,0,775448786,0,0 4,0,790338525,0,0 5,0,746673839,0,0 6,0,836514780,0,0 7,0,736872137,0,0 8,0,676292951,0,0 9,0,669155517,0,0 10,0,701372996,0,0 11,0,615672275,0,0 12,0,698614761,0,0 13,0,728031845,0,0 14,0,722970987,0,0 15,0,498719471,0,0
Would be nice to support the other format
Hi, there is no problem using the format like "chr1A" in my case. Maybe, the format of your input file is not right, try again or send me all the input files and codes (haozd1992@163.com).
I've tried the following with this karyotype file:
and got the following error:
So I have to modify my karyotype as follow:
Would be nice to support the other format