Question: Ideogram not alligned with ggbio and tracks()
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gravatar for my4
3.3 years ago by
my40
my40 wrote:

Hello,

I am using ggbio to plot a series of genomic tracks with a shared genomic x-axis.  As described in the ggbio documentation, I am using the tracks() function to align them.  I had expected that when I added an Ideogram using the Ideogram() function, that it would be aligned with this genomic axis.  However this does not appear to be the case.  So my question is, how can I add an ideogram to tracks so that it is aligned with other plots.

To make this clear I am trying to draw three plots looking like this:

IDEOGRAM

Data Track 1

Data Track 2

Both data tracks have the same x-axis (some chromosome) and are aligned well by the tracks() function.  The ideogram draws, but is clearly not aligned in the same way.  I know this as the ideogram is a different length to the data tracks, the centromeres do not line up.  I am using hg19 if that matters.

Alternatively, is there another way to draw an ideogram and align a common x-axis across multiple plots using ggplot2?

Cheers,

Matt

ggbio ggplot2 • 840 views
ADD COMMENTlink modified 2.9 years ago by oswaldo.lorenzo10 • written 3.3 years ago by my40
Answer: Ideogram not alligned with ggbio and tracks()
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gravatar for oswaldo.lorenzo
2.9 years ago by
oswaldo.lorenzo10 wrote:

Try to fix the original data tracks.

fixed(IDEOGRAM) <- TRUE

fixed(Data Track 1) <- TRUE

fixed(Data Track 2) <- TRUE

 

tracks(IDEOGRAM, Data Track 1, Data Track 2)

 

Best,

 

 

 

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by oswaldo.lorenzo10
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