OmicCircos - Error in 1:scale.n : NA/NaN argument
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Entering edit mode
@stefan-langenberg-12599
Last seen 4.5 years ago

Dear all,

I am trying to use package OmicCircos to create a circular genome plot. However, I am getting some strange results, I can not explain: some data at the end are displayed in the wrong segment. To find evidence if this error is caused by the data or by an error in package OmicCircos, I am trying to create a circos-plot with a subset of the data, where the error occurs:

library(OmicCircos)


library(OmicCircos)

seg.f <-
structurelistseg.name = c("17", "17", "17", "17", "17", "17", 
"17", "17", "17", "17", "17", "18", "18", "18", "18", "18", "18", 
"18", "18", "18", "18", "18", "19", "19", "19", "19", "20", "21", 
"22", "22", "23", "24", "25", "26", "27"), seg.Start = c(0L, 
1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 0L, 1L, 2L, 3L, 4L, 
5L, 6L, 7L, 8L, 9L, 10L, 0L, 1L, 2L, 3L, 0L, 0L, 0L, 1L, 0L, 
0L, 0L, 0L, 0L), seg.End = c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 
9L, 10L, 11L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 1L, 
2L, 3L, 4L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L), the.v = c(NA, 
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 
NA, NA), NO = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 
NA, NA, NA, NA, NA, NA, NA)), .Names = c("seg.name", "seg.Start", 
"seg.End", "the.v", "NO"), row.names = c(NA, 35L), class = "data.frame")

seg.v <-
structurelistseg.name = c("17", "17", "17", "17", "17", "17", 
"17", "17", "17", "17", "17", "18", "18", "18", "18", "18", "18", 
"18", "18", "18", "18", "18", "19", "19", "19", "19", "20", "21", 
"22", "22", "23", "24", "25", "26", "27"), seg.po = c(1L, 2L, 
3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 1L, 2L, 3L, 4L, 5L, 6L, 
7L, 8L, 9L, 10L, 11L, 1L, 2L, 3L, 4L, 1L, 1L, 1L, 2L, 1L, 1L, 
1L, 1L, 1L)), .Names = c("seg.name", "seg.po"), row.names = c(NA, 
35L), class = "data.frame")

names <- levels(as.factor(seg.f$seg.name))
seg.num <- length(names)
colors   <- rainbow(seg.num, alpha=0.5);
db       <- segAnglePo(seg.f, names)

pdf("test.pdf")
par(mar=c(2, 2, 2, 2));
plot(c(1,800), c(1,800), type="n", axes=FALSE, xlab="", ylab="", main="");
circos(R=320, type="chr", cir=db, col=colors, print.chr.lab=TRUE, W=4, scale=TRUE);


 

When using the subset by running the code above, I am getting the error

Error in 1:scale.n : NA/NaN argument
In addition: Warning message:
In do.scale.cir(xc = xc, yc = yc, the.r = r + 10, total.num = total.num,  :
  NAs introduced by coercion to integer range

after the command

circos(R=320, type="chr", cir=db, col=colors, print.chr.lab=TRUE, W=4, scale=TRUE)

Any suggestion what has caused the error?

sessionInfo()

R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

locale:
[1] C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base     

other attached packages:
[1] OmicCircos_1.12.0    GenomicRanges_1.26.3 GenomeInfoDb_1.10.3
[4] IRanges_2.8.1        S4Vectors_0.12.1     BiocGenerics_0.20.0

loaded via a namespace (and not attached):
[1] zlibbioc_1.20.0      BiocInstaller_1.24.0 tools_3.3.0         
[4] XVector_0.14.0       RCurl_1.95-4.8       bitops_1.0-6        

Thanks in advance.

Regards Stefan

OmicCircos • 1.3k views
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Entering edit mode
The error message disappears when using the option
scale=FALSE
to to circos-command. It seems that circos does not deals correct with segments containing only one element.
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