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I am trying to use RIdeogram to generate a figure for the sugar pine genome using just the karyotype and labels (no heatmap), but... I keep running into the following error and warnings.
Error in if (min(diff(mydata)) >= myforce | tag == 3000) { :
missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In x[2] + x[3] : NAs produced by integer overflow
2: In x[2] + x[3] : NAs produced by integer overflow
3: In x[2] + x[3] : NAs produced by integer overflow
4: In x[2] + x[3] : NAs produced by integer overflow
I have a feeling the sugar pine genome might be too large? The total genome I'm working with is about 25 Gbp, the smallest full chromosome in the genome is 1.6 Gbp, but I get this error even when trying on two of the smallest "chromosomes" (as chr1 has already been split into halves because of limitations with other bioinformatics programs).
This is my input karyotype for this test on just the halves of chr1, as you can see the total length of chr1 is over 2.2 Gbp so I had to split it into two parts of roughly 1.1 Gbp. This is what the object chr1_karyotype outputs.
If this is indeed the error (genome being too large), do you know of a way I could work around this? If that is not the error, I would also greatly appreciate any help figuring out where I went wrong, Thank you.
The text was updated successfully, but these errors were encountered:
I am trying to use RIdeogram to generate a figure for the sugar pine genome using just the karyotype and labels (no heatmap), but... I keep running into the following error and warnings.
I have a feeling the sugar pine genome might be too large? The total genome I'm working with is about 25 Gbp, the smallest full chromosome in the genome is 1.6 Gbp, but I get this error even when trying on two of the smallest "chromosomes" (as chr1 has already been split into halves because of limitations with other bioinformatics programs).
This is my input karyotype for this test on just the halves of chr1, as you can see the total length of chr1 is over 2.2 Gbp so I had to split it into two parts of roughly 1.1 Gbp. This is what the object
chr1_karyotype
outputs.this is what the top of my dataframe with the label information
genes_chr1
looks likeand this is the command I am using just to check if the karyotype image is created without passing the labels as an argument, which it does
this is what chr1.png looks like:
but then when I try to add the label information with the following command I get the error I mentioned above
If this is indeed the error (genome being too large), do you know of a way I could work around this? If that is not the error, I would also greatly appreciate any help figuring out where I went wrong, Thank you.
The text was updated successfully, but these errors were encountered: