Question

circular genome visualisation: genomic.labels: Error in if (cr != chr) { : missing value where TRUE/FALSE needed

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chrisclarkson100 ▴ 50

@chrisclarkson100-11114

Last seen 2.6 years ago

United Kingdom

I am finding your circlize package really useful. However, I am trying to label certain parts of the genome in my circular diagram with the function "genomic.labels" and getting the highlighted error below:

library(circlize)

circos.initializeWithIdeogram(chromosome.index = paste0("chr", c(1:22,'X')))

circos.genomicDensity(data_from_bed1, col = c("#FF000080"), track.height = 0.1)

circos.genomicDensity(data_from_bed2, col = c("#B0E0E6"), track.height = 0.1)

circos.genomicLabels(differential_labels, labels.column=5, side = "inside",

cex=1.8,col = 'black', line_col='black')

Error in if (cr != chr) { : missing value where TRUE/FALSE needed

The data from the differential_labels variable is just a normal bed file format. e.g.

1 chr1 10011 10526 277 chr1_10011_10526

2 chr1 31904591 31905068 497 chr1_31904591_31905068

3 chr1 108113082 108113613 259 chr1_108113082_108113613

4 chr1 143366525 143366833 219 chr1_143366525_143366833

5 chr1 149032152 149036235 214 chr1_149032152_149036235

6 chr1 235680770 235681860 205 chr1_235680770_235681860

7 chr1 236260392 236260727 230 chr1_236260392_236260727

8 chr1 240347680 240348538 254 chr1_240347680_240348538

9 chr1 248571411 248572287 310 chr1_248571411_248572287

10 chr10 42354937 42385067 528 chr10_42354937_42385067

When I try this with code (using an example for from the package vignette (Chapter 11 figure 11.3)) using data from a randomly generated bed file it works fine....

circos.initializeWithIdeogram()

bed = generateRandomBed(nr = 50, fun = function(k) sample(letters, k, replace = TRUE))
bed[1, 4] = "aaaaa"
circos.genomicLabels(bed, labels.column = 4, side = "inside")
circos.clear()

Can anyone help me out?

genomicfeatures rcircos • 1.6k views

ADD COMMENT • link 6.9 years ago chrisclarkson100 ▴ 50

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Dear Chris,

Hope you are well. I am facing the same problem. Did you resolve this? If so, could you please help me?

Cheers Naveen

ADD REPLY • link 5.8 years ago whizkid996 • 0

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Hi Naveen, Sorry I'm so late to reply- I haven't been logged into this site for ages... I went through my notes on this project and I think that I just gave up on trying to fit 2 genomic density profiles and labels all in one plot... Instead I just went for one genomic density profile and labels on the inner ring and this seemed to fit.

Also their may have been a problem with the ordering/ sorting of the bed file used to input the label locations...

I had to sort it as follows:

head(bedfile_labels)
chr10    2000    3000    green
chr10    4000    5000    red

ord=data.frame()
for(i in c(1:22,c('X'))){
  tmp=bedfile_labels[gsub('chr','',genes$V1)==i,]
  ord=rbind(ord,tmp[order(tmp$V2),])
}

.....
circos.genomicLabels(bedfile_labels, labels.column = 4, side = "inside", cex=1.8,
                     col = ord$color,line_col = ord$color)

I'm sorry about the lateness.... I hope this helps- but it was so long ago that I wrote the code that it might not be helpful

ADD REPLY • link 5.6 years ago chrisclarkson100 ▴ 50