Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a QC step (NO LONGER MANTAINED)
It's not really an "issue" per se, but I have found it useful to change the blob size based upon the length of the contig or scaffold that has been mapped to your reads... I've done this on two projects where we are interested in one taxa only out of a bunch of other that are essentially "contamination".
To do it, I simply change this line in makeblobplot.R
From:
g <- g + geom_point(data=mfilt[mfilt[,taxlevel]==t,],aes_string(x="gc", y="cov", colour=taxlevel), size=2, alpha=I(1/3))
to:
g <- g + geom_point(data=mfilt[mfilt[,taxlevel]==t,],aes_string(x="gc", y="cov", colour=taxlevel, size="len"), alpha=I(1/3))
It's not really an "issue" per se, but I have found it useful to change the blob size based upon the length of the contig or scaffold that has been mapped to your reads... I've done this on two projects where we are interested in one taxa only out of a bunch of other that are essentially "contamination".
To do it, I simply change this line in makeblobplot.R
From:
g <- g + geom_point(data=mfilt[mfilt[,taxlevel]==t,],aes_string(x="gc", y="cov", colour=taxlevel), size=2, alpha=I(1/3))
to: g <- g + geom_point(data=mfilt[mfilt[,taxlevel]==t,],aes_string(x="gc", y="cov", colour=taxlevel, size="len"), alpha=I(1/3))