R circlize package problem with drawing histogram
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2.1 years ago
marvel479 • 0

Forgive my confusion, but I can't figure out the correct usage of circlize to draw a histogram. I want to draw a histogram for one of its tracks and would like to use my read counts for Y-axis, and the x should be the genomic position, however wide or narrow. The syntax however is:

circos.trackHist(factors, x, ....)

that doesn't work though. How should I imply that my x should have chromosome no., start and stop position information, the bin height being no. of reads, for each row?

I am assuming I can write:

circos.trackHist(factors = mydataframe$reads, x = x)

This is what my file looks like: head(dataframe)

 Chrom     Start       End Reads
1  chr1  42938268  42938392     2
2  chr1  63224349  63225050     2
3  chr1  71646172  71646228     2
4  chr1  72904979  72905055     2
5  chr1 138065763 138065817     2
6  chr1 164635940 164635994     2
R genome circlize Rcirc Circos • 616 views
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It might be better to ask this on https://support.bioconductor.org/ - the developer is more active there.

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Seems that the user went there: https://support.bioconductor.org/p/129496/ Thanks @RamRS

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Thanks @RamRS and @Kevin Blighe. I did put a post to https://support.bioconductor.org/

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Please do not add an answer unless you're answering the principal question. This should have been a comment and I have moved it to one now, but please be more careful in the future.

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