Question: OmicCircos barplot height and scale
gravatar for Miss Agnieszka Aleksandra Golicz
2.4 years ago by


I'm trying to use OmicCircos to plot log(FPKM) as a barplot.  It seems to be working fine, other than the barplot seems to have a default height even if the the value of expression is 0. This can be seen when I add scale. 0 on the scale corresponds to an already sizable bar. This gives a false impression of expression where in fact there is none. I have attached code and a sample plot ( I would like the bar corresponding to 0 expression to have no height. In other words, 0 on the scale to correspond to base line where the bottom of the bar sits. Is that possible? Also I was wondering if it is possible to change scale color?


circos(R=360, W=40, cir=db, mapping=tr1, col.v=3, type="b", B=FALSE, col=c1, lwd=0.1, scale=TRUE)
circos(R=320, W=40, cir=db, mapping=tr2, col.v=3, type="b", B=FALSE, col=c2, lwd=0.1, scale=TRUE)
circos(R=280, W=40, cir=db, mapping=tr3, col.v=3, type="b", B=FALSE, col=c3, lwd=0.1, scale=TRUE)
circos(R=240, W=40, cir=db, mapping=tr4, col.v=3, type="b", B=FALSE, col=c4, lwd=0.1, scale=TRUE)
circos(R=200, W=40, cir=db, mapping=tr5, col.v=3, type="b", B=FALSE, col=c5, lwd=0.1, scale=TRUE)
circos(R=160, W=40, cir=db, mapping=tr6, col.v=3, type="b", B=FALSE, col=c6, lwd=0.1, scale=TRUE)
circos(R=120, W=40, cir=db, mapping=tr7, col.v=3, type="b", B=FALSE, col=c7, lwd=0.1, scale=TRUE)
circos(R=80, W=40, cir=db, mapping=tr8, col.v=3, type="b", B=FALSE, col=c8, lwd=0.1, scale=TRUE)
circos(R=40, W=40, cir=db, mapping=tr9, col.v=3, type="b", B=FALSE, col=c9, lwd=0.1, scale=TRUE)

R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 14393)

[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252   
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C                      
[5] LC_TIME=English_Australia.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RColorBrewer_1.1-2   OmicCircos_1.12.0    GenomicRanges_1.26.2 GenomeInfoDb_1.10.2 
[5] IRanges_2.8.1        S4Vectors_0.12.1     BiocGenerics_0.20.0 

loaded via a namespace (and not attached):
[1] zlibbioc_1.20.0 XVector_0.14.0  gtable_0.2.0    grid_3.3.2     

omiccircos • 537 views
ADD COMMENTlink written 2.4 years ago by Miss Agnieszka Aleksandra Golicz40
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 263 users visited in the last hour