Question: Rcircos for Multiple tracks of Expression data
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gravatar for yifangt86
3 months ago by
yifangt860
USA
yifangt860 wrote:

Hello I am trying to plot expression data with Rcircos without an ideogram information. My dataframe is like this:

Chr     Start   End     Band            CSR1    CSR2    CSR3    MTR1    MTR2    MTR3
chr5B   16521   20994   AeCS5B01G000100 1821.8  739.6   1234.0  1146.2  1380.0  1229.4
chr5B   60616   61023   AeCS5B01G000200 104.2   60.0    30.2    17.2    56.0    43.1
chr5B   87107   88168   AeCS5B01G000300 0.0     0.0     0.0     0.0     0.0     0.0
chr5B   210311  215424  AeCS5B01G000400 519.4   191.7   306.1   353.8   277.1   386.2
chr5B   217914  219359  AeCS5B01G000500 322.7   79.9    237.0   201.1   276.6   265.3
chr5B   229460  233000  AeCS5B01G000600 497.8   261.9   436.8   625.3   403.7   278.7

I want to visualize the 6 samples as 6 tracks as from RCircos. The reason I do not have the ideogram is the genome is from de novo assembly with an approximate annotation, so that the gene coordinates may overlap to each other which violates the requirement of RCircos Ideogram. I appreciate any experience with this scenario. Thanks a lot!

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