Question: OmicCircos barplot height and scale
0
gravatar for Miss Agnieszka Aleksandra Golicz
2.2 years ago by
Australia

Hi,

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 (https://s28.postimg.org/n8sqg3znx/circos.png). 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?

Agnieszka

par(mar=c(4,4,4,4))
plot(c(1,800),c(1,800),type="n",axes=FALSE,xlab="",ylab="",main="")
circos(R=400,cir=db,type="chr",col=colors,print.chr.lab=TRUE,W=4)
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)

locale:
[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 • 512 views
ADD COMMENTlink written 2.2 years ago by Miss Agnieszka Aleksandra Golicz40
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