Entering edit mode
7.3 years ago
yifangt86
▴
60
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!